On 7/21/12 2:13 AM, Mark Abraham wrote:
On 21/07/2012 3:44 PM, radhika jaswal wrote:
When replying to a digest, do change the subject to something useful, and do not
include the entire digest in your email. People have better things to do than
scroll through lots of text to find the relevant part.
Dear Sir,
I am using the ffG43a1 force field. Mine is an unusual unusual peptide and got
the necessary files from prodrg server.
So perhaps you should examine its output and see whether hybridization makes
sense then, before you worry about doing anything else. Garbage from a broken
earlier step causes garbage later. If you aren't using prodrg properly,
everything else is irrelevant.
and also pasting the top file. Please tell where , m making the mistake.
Unfortunately that's impossible, because you are #including topology files that
you are not showing us, nor have you described your molecule to us. Likely
nmab2.itp is not well formed.
Indeed, PRODRG produces very unreliable output and you should not use its
topologies without considerable modifications. Amino acid residues will have
parameters that are completely wrong.
http://pubs.acs.org/doi/abs/10.1021/ci100335w
-Justin
The Force Fields to be included
#include "ffG43a1.itp"
; Include nmab2 topology
#include "nmab2.itp"
; Include water topology
#include "spc.itp"
; Include position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
#ifdef POSRE_WATER
; Position Restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
These position restraints sections are not correctly located, but this is not
your problem right now. See
http://www.gromacs.org/Documentation/How-tos/Position_Restraints
Mark
[ system ]
; Name
DRG in water
[ molecules ]
; Compound #mols
DRG 1
SOL 397
Thanks Sir.
Radhika
--
========================================
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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