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.
On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul jalem...@vt.edu wrote:
Biswajit Gorai 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
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
A lot of thanks to your charitable mood now the things has been resolved :) .
Thanks again.
On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul jalem...@vt.edu wrote:
bipin singh wrote:
Thanks again
For the record, I didn't ask that you send me your files so I could
troubleshoot for you.
Thanks for your inputs.
I have followed your suggestion and included the .itp for the octane
molecule (containing atomtype definition for new atoms) in the
topology file(.top) of the whole system (prot+oct+water). but during
grompp it produce error and results in termination due to non matching
bipin singh wrote:
Thanks for your inputs.
I have followed your suggestion and included the .itp for the octane
molecule (containing atomtype definition for new atoms) in the
topology file(.top) of the whole system (prot+oct+water). but during
grompp it produce error and results in termination
Thanks for your suggestions.
Now I am getting the following error during grompp
Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not
match (C1 - N)
Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not
match (C2 - CA)
Warning: atom name 6 in topol.top and
bipin singh wrote:
Thanks for your suggestions.
Now I am getting the following error during grompp
Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not
match (C1 - N)
Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not
match (C2 - CA)
Warning: atom name 6 in
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*
; Include water
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
On 2012-03-26 13:55, bipin singh wrote:
Hello all,
I am using the GAFF topology provided for octan-1-ol at Gromacs liquid
database (http://virtualchemistry.org/molecules/111-87-5/index.php). I
have incorporated all the parameters
for atoms, bonds and non-bonded interaction type in the
Thanks for your reply.
But as far as I understood, in order to use these GAFF topology (for
e.g. to perform simulation using these topologies) with Gromacs we
have to incorporate the information from these topologies to the
existing Amber forcefields in Gromacs or Is there anyway (Possibility
of
bipin singh wrote:
Thanks for your reply.
But as far as I understood, in order to use these GAFF topology (for
e.g. to perform simulation using these topologies) with Gromacs we
have to incorporate the information from these topologies to the
existing Amber forcefields in Gromacs or Is there
Thanks for your reply.
Yes, you are right that these topologies are self supporting and there
is no need to to call any other information. I followed your
suggestions and able to generate a biphasic system of water/octane
containing a protein molecule. But, when I tried grompp on this
biphasic
bipin singh wrote:
Thanks for your reply.
Yes, you are right that these topologies are self supporting and there
is no need to to call any other information. I followed your
suggestions and able to generate a biphasic system of water/octane
containing a protein molecule. But, when I tried
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