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 <jalem...@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 <jalem...@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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