[gmx-users] all-angle constraints
Mark.Abraham at anu.edu.au
Sat Jul 21 08:13:10 CEST 2012
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.
> 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"
> #ifdef POSRE_WATER
> ; Position Restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
These position restraints sections are not correctly located, but this
is not your problem right now. See
> [ system ]
> ; Name
> DRG in water
> [ molecules ]
> ; Compound #mols
> DRG 1
> SOL 397
> Thanks Sir.
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