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 <jalem...@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.vic...@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...@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...@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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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