Re: C36 force field

From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Tue Dec 11 2018 - 11:16:31 CST

Dear João,
Thank you so much for your help and support.

-- 
Regards, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "João Ribeiro" <jribeiro_at_ks.uiuc.edu> 
To: "shekaari" <shekaari_at_email.kntu.ac.ir> 
Cc: "namd-l" <namd-l_at_ks.uiuc.edu> 
Sent: Tuesday, December 11, 2018 8:25:00 PM 
Subject: Re: namd-l: C36 force field 
Dear Ashkan, 
P l ease keep namd-l @ [ http://ks.uiuc.edu/ | ks.uiuc.edu ] in the CC list so we can keep track of the discussion and others can benefit from it as well. 
if the simulation works fine using a parameter file from a previous CHARMM version is because you are probably mixing topologies from different CHARMM versions in the structure preparation phase, which you should not do . You should consistently use the same CHARMM ff version during preparation and run phases. I would suggest CHARMM36. 
Best 
João 
On Tue, Dec 11, 2018 at 10:32 AM Ashkan Shekaari < [ mailto:shekaari_at_email.kntu.ac.ir | shekaari_at_email.kntu.ac.ir ] > wrote: 
Dear João, 
Thank you so much for your help. I can now generate the psf file using multiple topology files. 
However, in minimization or equilibration processes, despite using the feature of importing several parameter files in .conf file as below: 
# FORCE-FIELD PARAMETERS ## 
######################################################## 
parameters ../solvation/par_all36_prot.prm 
parameters ../solvation/par_all36_lipid.prm 
parameters ../solvation/par_all36_na.prm 
I get the error message stating that 
Charm++ fatal error: 
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB. 
This is while importing 
parameters ../solvation/par_all27_prot_lipid_na.inp 
works. That is why I am looking for a single file containing prot, lipid, and na 
just like par_all27_prot_lipid_na.inp prepared in NAMD tutorial files. 
-- 
Best regards, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "João Ribeiro" < [ mailto:jribeiro_at_ks.uiuc.edu | jribeiro_at_ks.uiuc.edu ] > 
To: "namd-l" < [ mailto:namd-l_at_ks.uiuc.edu | namd-l_at_ks.uiuc.edu ] >, "shekaari" < [ mailto:shekaari_at_email.kntu.ac.ir | shekaari_at_email.kntu.ac.ir ] > 
Sent: Tuesday, December 11, 2018 6:53:31 PM 
Subject: Re: namd-l: C36 force field 
Dear Ashkan, 
you might be getting confused about what you can and can't do. In your psfgen script, you can load more that one topology (or stream file) when building your structure. Just repeat the command "topology <topology/stream file>", like 
" 
.. 
topology top_all36_lipid.rtf 
topology top_all36_prot.rtf 
.. 
" 
You will only need the parameters to actually run the simulation. 
I hope this helps 
Best 
João 
On Tue, Dec 11, 2018 at 7:39 AM Ashkan Shekaari < [ mailto:shekaari_at_email.kntu.ac.ir | shekaari_at_email.kntu.ac.ir ] > wrote: 
BQ_BEGIN
Dear experts, 
Is there any CHARMM36 all-hydrogen parameter file for both proteins and lipids written in a single file? 
For prot, lipid, and na, there are three separate files, and therefore, I cannot generate the psf file of my protein. 
-- 
Regards, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
-- 
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……………………………………………………... 
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Theoretical and Computational Biophysics Group 
Beckman Institute, University of Illinois 
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[ mailto:jribeiro_at_ks.uiuc.edu | jribeiro_at_ks.uiuc.edu ] 
+1 (217) 300 5851 
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……………………………………………………... 
João Vieira Ribeiro 
Theoretical and Computational Biophysics Group 
Beckman Institute, University of Illinois 
[ http://www.ks.uiuc.edu/~jribeiro/ | http://www.ks.uiuc.edu/~jribeiro/ ] 
[ mailto:jribeiro_at_ks.uiuc.edu | jribeiro_at_ks.uiuc.edu ] 
+1 (217) 300 5851 

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