[gmx-users] all-angle constraints

[Mark Abraham]

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"
> #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
>