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

[Justin A. Lemkul]

bipin singh wrote:
> 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.
> 

Looking closer at the error, what's happening is your octanol molecule is in a 
place where the topology expects the amino acid sequence Ser-Leu.  Perhaps that 
will help you track down the source of the problem.  It seems to me that your 
octanol molecule occurs earlier in the coordinate file than it does in the topology.

If you still can't locate the problem, then you can always start over building 
your system in a known order, checking the alignment of the coordinate file and 
topology at every step.

-Justin

> 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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> 
> 
> 

-- 
========================================

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

========================================