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

[Justin A. Lemkul]

bipin singh wrote:
> Thanks again
> 

For the record, I didn't ask that you send me your files so I could troubleshoot 
for you.  Luckily for you I'm in a charitable mood this morning, so I took a look ;)

Your problem is that you have a [molecules] directive in oct.itp.  Please refer 
to the documentation for the difference between a .top topology and a .itp topology:

http://www.gromacs.org/Documentation/File_Formats/.itp_File

The presence of this [molecules] directive tells grompp that the first thing it 
should expect is a block of octanol, when in fact your coordinate file has the 
protein first (starting with Ser-Leu, as I suspected).  You then have "1-octanol 
1" in your topol.top, which says you're including another random octanol 
molecule somewhere later.

You need a single [molecules] directive in the .top, which must match the order 
of the coordinate file.  Once you've got that, things should work fine.

-Justin

>>From the error It seems that I have placed the octane molecule before
> the protein but it is not the case, I dont know why grompp is reading
> parameters for octane first and expecting it to match with protein. I
> know that its my problem and I have to think about
> that but just for the reference for you I am attaching the coordinate
> and topology files.
> 
> On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> 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
>>
>> ========================================
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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

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