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

[Kalyanashis Jana]

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..

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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-- 
Kalyanashis Jana
email: kalyan.chem.in at gmail.com