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

[bipin singh]

A lot of thanks to your "charitable mood" now the things has been resolved :) .
Thanks again.

On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
> --
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-- 
-----------------------
Regards,
Bipin Singh