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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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