From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Feb 05 2020 - 09:18:50 CST
Dear Santanu,
Psfgen is distributed in VMD as a TCL package/plugin, which you use from within VMD. You don’t execute the psfgen executable.
Please install VMD, and open VMD, on the main window: Extensions -> TkConsole. Navigate to the folder you have your psfgen script and necessary files, and execute the following command: “play <my psfgen input file>”
You can also execute VMD in text mode: “vmd -dispdev text -e <my psfgen input file>”. https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html
I hope this helps.
Best,
João
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Santanu Santra <santop420_at_gmail.com>
Reply-To: <namd-l_at_ks.uiuc.edu>, Santanu Santra <santop420_at_gmail.com>
Date: Wednesday, February 5, 2020 at 8:42 AM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Cc: <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
Hello sir, thanks for the reply.
But I am stuck to few silly problems.
I downloaded vmd-1.9.4a38.src.tar.gz and vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz . Once I untar them, either of two contains one plugin folder. Even in vmd-1.9.4a38.src.tar.gz , one directory is present in the name of psfgen. I could not find any executable in the name of psfgen. Kindly guide me to get the executable of psfgen. Apart from that everything you have suggested in the last mail is clear to me and I made the script file ready.
If possible can you please attach the executable of psfgen.
Many many thanks in advance for your help sir.
Regards.
Santanu Santra
On Tue, Feb 4, 2020 at 8:32 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:
Hi Santanu
The psfgen log had the information the I information that I was about to ask.
To prepare structures using Drude forcefield, you need to use the latest version of psfgen (version 2.0) distributed with the alpha version of VMD. Psfgen will be updated on the NAMD side soon.
Please add the line “auto angle dihedral” to the segment section of your psfgen script, and “vpbonds 0” after resetpsf command. Please check the manual for more information about these commands (https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf)
I hope this helps.
Best,
João
From: Santanu Santra <santop420_at_gmail.com>
Date: Tuesday, February 4, 2020 at 6:32 AM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Cc: <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
Hello sir,
In addition to my previous email, I have also tried with nightly build version of NAMD, but still the same error is coming. For clarification of the issue, I am attaching the files::
=======================================================================
my psfgen input file code ::
-------------------------------------------------------------
package require psfgen
resetpsf
topology toppar_drude_master_protein_2013f.str
segment INA {
first GNTE
pdb ins_A.pdb
last CTER
}
coordpdb ins_A.pdb INA
guesscoord
writepdb drude_prot_vac.pdb
writepsf drude_prot_vac.psf
----------------------------------------------------------
==========================================
============================================
The psfgen log file ::
------------------------------------------
psfgen_out.log (attached herewith)
-------------------------------------------
Any kind of help is highly appreciated.
Thanks and Regards
Santanu Santra
On Tue, Feb 4, 2020 at 10:13 AM Santanu Santra <santop420_at_gmail.com> wrote:
Hi Sir,
Thanks for the reply. Currently I'm using NAMD 2.12 . In my psf file "auto angles dihedrals" segment is present for protein. Again I have created the structure with vpbonds 0 but same problem is coming during minimization.
I have a gentle query::
In ANGLE section "CD2O1A OD2C1A LPDO1" combination is absent. So is it required to put the values for those combinations including lone pairs from any other resources or it will automatically take care of that?
Thanks and regards
Santanu Santra
On Mon, Feb 3, 2020 at 9:37 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:
Before I forget again,
Please make sure that you have the line “auto angles dihedrals” when building your protein segment(s).
Best,
João
From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Date: Monday, February 3, 2020 at 9:50 AM
To: <namd-l_at_ks.uiuc.edu>, Santanu Santra <santop420_at_gmail.com>
Subject: Re: namd-l: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
Hi Santanu,
A couple of questions:
Did you prepare the structure with the option vpbonds 0?
Which version of NAMD are your running? Did you try the nightly build?
Best,
João
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Santanu Santra <santop420_at_gmail.com>
Reply-To: <namd-l_at_ks.uiuc.edu>, Santanu Santra <santop420_at_gmail.com>
Date: Sunday, February 2, 2020 at 10:24 PM
To: <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
The error is coming for every lone pairs :::
Another error log is
==========================
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 (ATOMS 8 9 11)
Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 (ATOMS 8 9 11)
Aborted (core dumped)
======================================
thanks for any help
santanu santra
On Mon, Feb 3, 2020 at 9:30 AM Santanu Santra <santop420_at_gmail.com> wrote:
Hi everyone,
I tried to model one model protein in drude forcefield (toppar_drude_master_protein_2013f.str) and successfully generated the structure by psfgen. But when I am trying to minimize it in namd, it is showing some error throwing message of "unable to find the angle parameter for lone pairs and two other atoms". I checked the ANGLE section in the *.str file to find the combination of these three atoms but it was not there.
Can anyone please suggest me where from I can get the Ktheta and Theta0values for those angles including lone pair as one of these three atoms.
Exact error log is ::::
=====================================================
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR LPD OD2C1A LPD (ATOMS 91 87 92)
Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR LPD OD2C1A LPD (ATOMS 91 87 92)
Aborted (core dumped)
==================================================
The section of pdb for which it is throwing error is as follows :
================================================
ATOM 8 C GLY 1 -2.504 6.616 3.758 1.00 0.00 XXX C
ATOM 9 O GLY 1 -1.357 7.045 3.786 1.00 0.00 XXX O
ATOM 10 LPOA GLY 1 -0.585 6.409 3.797 0.00 0.00 XXX H
ATOM 11 LPOB GLY 1 -1.192 8.031 3.797 0.00 0.00 XXX H
===========================================================
Any kind of suggestion is highly accepted.
Thanks and regards
Santanu Santra
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