VMD-L Mailing List
From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Tue May 28 2019 - 09:16:46 CDT
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- Previous message: Joao Ribeiro: "Re: Re: psfgen problems of many segment complex"
- In reply to: Joao Ribeiro: "Re: Re: psfgen problems of many segment complex"
- Next in thread: Takeru KAMEDA: "Re: Re: psfgen problems of many segment complex"
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Dear João
Thank you for your advising.
(And, I'm sorry I sent the same email twice. I don't remember I sent it ... )
I tried your recommended command, following message were shown :
========================================================
.....
.....
.....
psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_YP1.pdb for segment YP1
psfgen) Warning: failed to set coordinate for atom O ASP:135 YP1
segfiles psfgen_formatted_autopsf-temp.pdb_AP1.pdb psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen
_formatted_autopsf-temp.pdb_VP1.pdb psfgen_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP6.pdb psfgen_formatted_autopsf-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_ZP1.pdb
31786 32343
psfgen) building segment ZP1
psfgen) reading residues from pdb file psfgen_formatted_autopsf-temp.pdb_ZP1.pdb
psfgen) extracted 70 residues from pdb file
psfgen) setting patch for first residue to NTER
psfgen) setting patch for last residue to CTER
psfgen) Info: generating structure...psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) Info: skipping bond C-N at end of segment.
psfgen) Info: skipping improper C-CA-N-O at end of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
psfgen) Info: skipping conformation N-CA-C-O at end of segment.
psfgen) Info: skipping conformation N-CA-C-N at end of segment.
ZP1:105
ZP1:36
segment complete.
psfgen) reading coordinates from pdb file psfgen_formatted_autopsf-temp.pdb_ZP1.pdb for segment ZP1
psfgen) Warning: failed to set coordinate for atom O THR:105 ZP1
segfiles psfgen_formatted_autopsf-temp.pdb_AP1.pdb psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen
_formatted_autopsf-temp.pdb_VP1.pdb psfgen_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatt!
ed_autop
s
f-temp.pdb_kP6.pdb psfgen_formatted_autopsf-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_aP1.pdb
32344 33113
psfgen) building segment aP1
Info) Coordinate I/O rate 0.20 frames/sec, 0 MB/sec, 5.1 sec
Info) Finished with coordinate file psfgen_formatted.pdb.
ERROR: Unable to open pdb file psfgen_formatted_autopsf-temp.pdb_aP1.pdb to read residues
========================================================
Such error occurs when the proccessing reachs to segment a (not A).
Previously, we performed usual psfgen, an error was shown in the case of segment a.
Thank you in advance.
Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan
________________________________________
差出人: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
送信日時: 2019年5月28日 22:45
宛先: Takeru KAMEDA; Peter Freddolino
CC: vmd-l_at_ks.uiuc.edu
件名: Re: vmd-l: Re: psfgen problems of many segment complex
Dear Takeru,
Please try :"autopsf -protein -nucleic -prefix psfgen -top [list ./../toppar/top_all36_na.rtf ./../toppar/top_all36_prot.rtf ./../toppar/top_all36_carb.rtf ./../toppar/top_all36_lipid.rtf]"
Basically, every time the -top flag, the list of topology files to be loaded is initialized.
Best
João
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
https://jpn01.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~jribeiro%2F&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Ca0a6985d6d19405f8cef08d6e372c028%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636946479336972016&sdata=VXwlr5KboP9kTDjO42HY%2Byk3YM73Z33c4liPP219488%3D&reserved=0
jribeiro_at_illinois.edu
+1 (217) 3005851
On 5/28/19, 8:28 AM, "Takeru KAMEDA" <owner-vmd-l_at_ks.uiuc.edu on behalf of kamedapon_at_hiroshima-u.ac.jp> wrote:
Dear Peter
Thank you for your advising.
We tried following command :
=========================================================
resetpsf
autopsf -protein -nucleic -prefix psfgen -top ./../toppar/top_all36_na.rtf -top ./../toppar/top_all36_prot.rtf -top ./../toppar/top_all36_carb.rtf -top ./../toppar/top_all36_lipid.rtf
=========================================================
and GUI interface.
However, following error was print :
=========================================================
segfiles psfgen_formatted_autopsf-temp.pdb_AP1.pdb psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb ps
fgen_formatted_autopsf-temp.pdb_VP1.pdb psfgen_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_for!
matt!
ed_autop
sf-temp.pdb_kP6.pdb psfgen_formatted_autopsf-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_AP1.pdb
1 1625
psfgen) building segment AP1
psfgen) reading residues from pdb file psfgen_formatted_autopsf-temp.pdb_AP1.pdb
psfgen) extracted 97 residues from pdb file
psfgen) setting patch for first residue to NTER
psfgen) setting patch for last residue to CTER
psfgen) Info: generating structure...psfgen) unknown patch type CTER
failed!
Info) Coordinate I/O rate 0.19 frames/sec, 0 MB/sec, 5.2 sec
Info) Finished with coordinate file psfgen_formatted.pdb.
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
=========================================================
Why such error was shown?
Any editing of PDB file are necessary ?
Thank you in advance.
Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan
________________________________________
差出人: Peter Freddolino <petefred_at_umich.edu>
送信日時: 2019年5月27日 22:47
宛先: Takeru KAMEDA
CC: vmd-l_at_ks.uiuc.edu
件名: Re: psfgen problems of many segment complex
You do not need to give segment names that are the same as the chain names in the pdb -- in fact I would advise against it. Autopsf, for example, just calls protein chains P1, P2, etc.
Best,
Peter
On Fri, May 24, 2019 at 11:14 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:
Dear VMD Users
Somehow my previous mail was not sent to the end (Sorry).
I have a question about how to apply psfgen to a complex with many segments.
We tried to use the structure (PDB: 3J81) with many segments (chains) as follows.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m 1 2 3
(https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2Fstructure%2F3j81&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Ca0a6985d6d19405f8cef08d6e372c028%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636946479336972016&sdata=5gIQe1ywL4ChYX8tfPq6qeU02r%2Frl5gb99eY%2B%2FALFlQ%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2Fstructure%2F3j81&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Ca0a6985d6d19405f8cef08d6e372c028%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636946479336972016&sdata=5gIQe1ywL4ChYX8tfPq6qeU02r%2Frl5gb99eY%2B%2FALFlQ%3D&reserved=0>)
However, we could not finish the psfgen script.
It seems that chain ID is case insensitive and hence e.g. chains A and a are regarded as duplicated chain IDs.
Could you tell me how to solve the problem?
We employed VMD 1.9.3 (psfgen version1.6.4), and CHARMM36 parameter. (https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmackerell.umaryland.edu%2Fcharmm_ff.shtml&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Ca0a6985d6d19405f8cef08d6e372c028%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636946479336972016&sdata=7wJIBnAbxhD41ivSoWNfFuVlpU3NfjJxaf1274FpgPg%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmackerell.umaryland.edu%2Fcharmm_ff.shtml&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Ca0a6985d6d19405f8cef08d6e372c028%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C636946479336972016&sdata=7wJIBnAbxhD41ivSoWNfFuVlpU3NfjJxaf1274FpgPg%3D&reserved=0>)
Thank you in advance.
Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan
The PSFgen script we used is as follows:
"""""""""""""""""""""""""""""""""""""""""""""""""
package require psfgen
resetpsf
topology ./../toppar/top_all36_na.rtf
topology ./../toppar/top_all36_prot.rtf
topology ./../toppar/top_all36_carb.rtf
topology ./../toppar/top_all36_cgenff.rtf
topology ./../toppar/top_all36_lipid.rtf
pdbalias residue A ADE
pdbalias residue G GUA
pdbalias residue C CYT
pdbalias residue T THY
pdbalias residue U URA
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
## protein
set sel [atomselect top protein]
set chains [lsort -unique [$sel get chain]] ;# return A B C D
foreach chain $chains {
puts "Adding protein chain $chain to psfgen"
set seg ${chain}PRO
set sel [atomselect top "protein and chain $chain"]
$sel set segid $seg
$sel writepdb tmp.pdb
segment $seg {
#first NTER
#last CTER
pdb tmp.pdb
}
coordpdb tmp.pdb
}
## RNA
set sel [atomselect top nucleic]
set chains [lsort -unique [$sel get chain]];# return A B C D
foreach chain $chains {
puts "Adding RNA chain $chain to psfgen"
set seg ${chain}RNA
set sel [atomselect top "nucleic and chain $chain"]
$sel set segid $seg
$sel writepdb tmp.pdb
segment $seg { pdb tmp.pdb }
set resids [lsort -unique [$sel get resid]]
#foreach r $resids {
#patch DEOX $seg:$r
#}
regenerate angles dihedrals
coordpdb tmp.pdb
}
guesscoord
writepsf psfgen.psf
writepdb psfgen.pdb
"""""""""""""""""""""""""""""""""""""""""""""""""
--
________________________________
差出人: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>>
送信日時: 2019年5月24日 21:52
宛先: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>; Takeru KAMEDA
件名: RE: psfgen problems of many segment complex
One segment at a time would be my advice. That's how the psfgen user guide does it (see page 4, where the protein BPTI is in a different segment than the water).
-Josh
On 2019-05-24 00:56:17-06:00 owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> wrote:
Dear VMD Users
I have a question about how to apply psfgen to a complex with many segments
- Next message: Peter Freddolino: "Re: Re: psfgen problems of many segment complex"
- Previous message: Joao Ribeiro: "Re: Re: psfgen problems of many segment complex"
- In reply to: Joao Ribeiro: "Re: Re: psfgen problems of many segment complex"
- Next in thread: Takeru KAMEDA: "Re: Re: psfgen problems of many segment complex"
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