[gmx-users] Energy minimization of an UNKNOWN molecule.

[Justin Lemkul]

On 11/3/14 12:57 AM, Kalyanashis Jana wrote:
> Thank you very much... But I am not going to use any parent molecules like
> protein or DNA. I would like to perform the gromacs simulation for this
> unknown molecule.
> First few lines of my topology file..
>
> ";
> ; File 'topol.top' was generated
> ; By user: kollan (506)
> ; On host: master.localdomain
> ; At date: Sun Nov  2 20:28:10 2014
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.6.3
> ;
> ; Command line was:
> ; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top
> ;
> ; Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> # include "A-T.itp"
>
> ; ----
> ; Built itp for A-T.mol2
> ;    by user vzoete     Mon Oct 27 06:32:46 CET 2014
> ; ----
> ;
>
> [ atomtypes ] "
>
>   The yellow colored lines are first seven line A-T.itp file And the error
> was
> ""Fatal error:
> Syntax error - File A-T.itp, line 7
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes"
>
> Please help me..
>

You'll need to show us what is in A-T.itp, because that's where the problem is. 
  Probably you're missing a [defaults] directive, but that's just a guess.

-Justin

> On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/2/14 11:32 AM, Kalyanashis Jana wrote:
>>
>>> Thank you so much... I have tried to run the grompp step according to you.
>>> But it is showing
>>> "Fatal error:
>>> Syntax error - File A-T.itp, line 7
>>> Last line read:
>>> '[ atomtypes ]'
>>> Invalid order for directive atomtypes"
>>> I have attached the .itp file and .top file.
>>> Please kindly tell me, what to do now..
>>>
>>>
>> Force-field level directives must be declared before molecule-level
>> directives.  So if your ligand requires new bonded or nonbonded parameters,
>> or new atom types, it must be #included before the declaration of any
>> [moleculetype].  So put your #include statement for the ligand topology
>> immediately after the #include statement for the parent force field.
>>
>> -Justin
>>
>>
>>   On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia <
>>> rosas.victor at gmail.com>
>>> wrote:
>>>
>>>   just put the itp file in your working directory, and include it in the
>>>> top file of your system, so that Gromacs can find it.
>>>>
>>>> Hope this helps.
>>>>
>>>> Victor
>>>>
>>>> 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana <kalyan.chem.in at gmail.com>:
>>>>
>>>>> Dear all,
>>>>> I am trying to run a gromacs simulation using an .itp file of an unknown
>>>>> molecule ( non protein and DNA). I don't want to put the .itp file in a
>>>>> forcefield folder and I would like put it in my working directory. Can
>>>>>
>>>> you
>>>>
>>>>> please tell me, what is procedure to finish the energy minimization?
>>>>>
>>>> Please
>>>>
>>>>> help me..
>>>>> Thanks in advance,
>>>>> Kalyanashis
>>>>>
>>>>> --
>>>>> Kalyanashis Jana
>>>>> email: kalyan.chem.in at gmail.com
>>>>> --
>>>>> Gromacs Users mailing list
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>>>
>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
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>
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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