VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue May 28 2019 - 08:45:26 CDT

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
http://www.ks.uiuc.edu/~jribeiro/
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://www.rcsb.org/structure/3j8145616433999940&sdata=R6X%2BZ4oNjCR5HH%2BebBb7GvLmhiac225ayiRvTrXXO84%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. (http://mackerell.umaryland.edu/charmm_ff.shtml0d3750%7C1%7C0%7C636945616434009934&sdata=wFXSZtV0nhA%2F%2FWuvUJviNV%2B0gXwWKuZtTY5JwD3%2FHR4%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