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

[Justin Lemkul]

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
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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

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