[gmx-users] Re: pdb2gmx error

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 27 20:02:06 CEST 2012

On 6/27/12 1:58 PM, Shima Arasteh wrote:
> Dear Shounak,
> So what's about the FOR residue? I can't eliminate it. I guess if I do as you suggest, I need to add the FOR to n.tdb and then the procedure would be different!

You do not need to add FOR to a .tdb entry.  These directives are only to modify 
protonation states of amines and carboxylates.  I believe you tried this before, 
and my comment was that such a procedure would not work (and it didn't).


> Yes, I added the FOR to rtp file on my own.
> Sincerely,
> Shima
> ----- Original Message -----
> From: shounakb <baners4 at rpi.edu>
> To: gmx-users at gromacs.org
> Cc:
> Sent: Wednesday, June 27, 2012 10:22 PM
> Subject: [gmx-users] Re: pdb2gmx error
> Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
> file works fine for the sequence you originally specified. (pdb2gmx executes
> without any errors)
> I guess you added the FOR cap's topology yourself?
> Justin, could this be an issue?
> Sincerely,
> Shounak
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998861.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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