[gmx-users] Re: How to add dihedral information from the GAFF topology

[bipin singh]

Thanks for your inputs.

I have checked the coordinate file thoroughly and the order of atoms
are same as defined in the [molecules] directive.
I really do not able to find out the source of the error.

On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Biswajit Gorai wrote:
>>
>> Dear Bipin,
>> Edit your topology file as:
>>
>> ###########################################
>> ; Include forcefield parameters
>> #include "amber99sb-ildn.ff/forcefield.itp"
>>
>> ; Include chain topologies
>> #include "topol_Protein_chain_A.itp"
>> #include "topol_Ion_chain_A2.itp"
>>
>> *#include "oct.itp"*
>>
>
> If oct.itp introduces new atom types (as the original .top does, for GAFF),
> placing this topology here will result in a fatal error since there is a new
> [atomtypes] directive that is introduced after the protein [moleculetype].
>  If oct.itp does not introduce any new atom types, its location within the
> system topology is irrelevant.
>
>> ; Include water topology
>> #include "amber99sb-ildn.ff/tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>  1    1       1000       1000       1000
>> #endif
>>
>> ; Include topology for ions
>> #include "amber99sb-ildn.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> Ion_chain_A2        1
>> *1-octanol         1
>> *
>> *SOL              8987*
>
>
> Depending on the order of the coordinate file, it may not be possible to
> merge the SOL entries in this way.
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
-----------------------
Regards,
Bipin Singh