Re: Regarding psf generation

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Oct 02 2019 - 10:21:48 CDT

Hi Shobhit, once again please keep namd-l in the loop.

 

Please read my answer to your previous email and try to answer those points, like, errors generated during the preparation, specific commands that you used, and so on. The description that you are providing is not enough.

 

Depending on the coarse grain model that you are using, autopsf might not be the perfect tool to prepare the psf and pdb. You might want to stick with psfgen only. Out of curiosity, did you try to go through one (or more) of our many tutorials (https://www.ks.uiuc.edu/Training/Tutorials/), in particular, NAMD Tutorial, Residue-Based Coarse-Graining, and Shape-Based Coarse Graining?

 

Best,

 

João

 

From: "SHOBHIT JAIN ." <f20150817_at_hyderabad.bits-pilani.ac.in>
Date: Wednesday, October 2, 2019 at 6:50 AM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Subject: Re: namd-l: Regarding psf generation

 

Sorry sir i wanted to ask that while i am generating a psf using autopsf tool for coarse grained model of protein + water that i have packed using packmol there the number of atom is increased in numbers and protein is getting disappeared after generation of psf.

 

On Tue, 1 Oct 2019, 19:40 Joao Ribeiro, <jribeiro_at_ks.uiuc.edu> wrote:

Please keep the namd-l mailing list in the loop so that others can benefit from the discussion. By the way, did you search in the namd-l and vmd-l archive for entries similar to your problem?

Once again, the details that you provided are not sufficient for any diagnostic. You need to send us the real problem, not describing your case in general and vague terms as “proper topology”. Also, please share the error messages that the program prints in the console. Most of the time, they are self-explanatory.

But let me try to guess here. When generating the psf and pdb files using psfgen, please make sure that your original pdb and topology file have the same residue name and atoms’ name. They need to match, otherwise, errors will occur.

 

Best,

 

João

From: "SHOBHIT JAIN ." <f20150817_at_hyderabad.bits-pilani.ac.in>
Date: Tuesday, October 1, 2019 at 3:28 AM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Subject: Re: namd-l: Regarding psf generation

 

Sir i was trying to generate the psf file for protein ligand complex by giving the proper topology file for ligand(generated using swissparam) also while generating psf file it is deleting some of ligand atoms.

 

On Mon, 30 Sep 2019, 23:24 Joao Ribeiro, <jribeiro_at_ks.uiuc.edu> wrote:

Dear Shobhit,

 

You will need to provide details of what and how you are doing so we can help you. Please provide as many details as you can.

Are all these messages related to the sphere model that you asked previously?

 

Best,

 

João

 

From: <owner-namd-l_at_ks.uiuc.edu> on behalf of "SHOBHIT JAIN ." <f20150817_at_hyderabad.bits-pilani.ac.in>
Reply-To: <namd-l_at_ks.uiuc.edu>, "SHOBHIT JAIN ." <f20150817_at_hyderabad.bits-pilani.ac.in>
Date: Monday, September 30, 2019 at 2:43 AM
To: <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Regarding psf generation

 

Dear sir/maam

I was trying to generate psf file form a pdb file. And i wasnt able to generate the psf file it is deleting some atom.

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