[gmx-users] Re: pdb2gmx error

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Jun 28 10:27:24 CEST 2012

Dear Justin,
Your suggestion of defining FVAL worked properly and at last I got the topology! :)
Thanks a llllllllllllllllooooooooooooooooooooooooooottttttttttttttttttttt! :)



----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, June 28, 2012 12:17 AM
Subject: Re: [gmx-users] Re: pdb2gmx error

On 6/27/12 2:42 PM, Shima Arasteh wrote:
> You are right.
> OK, the reason of adding FOR is what I explained a few minutes ago.
> All over, I'm supposed to use a modern FF . ( In similar researches I found CHARMM is suitable, so I would add FOR as the procedure explained in GROMACS.ORG)

This sounds like a good idea.

> For now, because I wanna regenerate an old simulation, I keep the FOR, then here it's stopped! Seeking for a solution!

There is one possible solution that I just thought of.  Rather than using FOR as its own residue, create a formylated valine, thus eliminating the problem with the call to CA of the preceding residue.

The .rtp entry:

[ FVAL ]
[ atoms ]
    CN   CH1   0.380     0
    ON     O  -0.380     0
     N     N  -0.280     1
     H     H   0.280     1
    CA   CH1   0.000     2
    CB   CH1   0.000     3
   CG1   CH3   0.000     4
   CG2   CH3   0.000     5
     C     C   0.380     6
     O     O  -0.380     6
[ bonds ]
    CN    ON
    CN     N
     N     H
     N    CA
    CA     C
     C     O
    CA    CB
    CB   CG1
    CB   CG2
[ impropers ]
     N    CN    CA     H
    CN   -CA     N    ON
    CA     N     C    CB
    CB   CG2   CG1    CA

The .hdb entry:

FVAL    1
1   1   H   N   CN  CA

Then add FVAL to residuetypes.dat as a protein residue.  Processing the .pdb file you posted before (merging FOR and VAL into FVAL and adjusting names according to the .rtp entry above) works correctly.

Disclaimer: this method "works" (i.e. produces a topology) but I do not necessarily endorse the use of the parameters shown.


-- ========================================

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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