[gmx-users] Re: pdb2gmx error
shima_arasteh2001 at yahoo.com
Thu Jun 28 10:27:24 CEST 2012
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 ]
[ impropers ]
N CN CA H
CN -CA N ON
CA N C CB
CB CG2 CG1 CA
The .hdb entry:
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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