On Tuesday, June 25, 2013 8:10 PM, Parker de Waal parker.dewaa...@kzoo.edu
wrote:
Now I've been able to successfully convert the two .mol2 files into gromacs
.itp however I am unsure how to convert the .frcmod file as well.
I'm sorry, but while topolbuild does convert *.mol2 files into
Hi Everyone,
I'm very interested in using a set of recently derived AMBER heme
topologies within GROMACS to perform MD simulation on P450 enzymes.
Specifically I would like to use parameters found here
https://gist.github.com/anonymous/995efe4d44c6cf0584ef
After trying to use topolbuild1.3,
On Wed, Jun 26, 2013 at 1:16 AM, Parker de Waal
parker.dewaa...@kzoo.edu wrote:
Hi Everyone,
I'm very interested in using a set of recently derived AMBER heme
topologies within GROMACS to perform MD simulation on P450 enzymes.
Specifically I would like to use parameters found here
Hi Mark,
That was silly mistake on my part... thank you for pointing that out.
Now I've been able to successfully convert the two .mol2 files into gromacs
.itp however I am unsure how to convert the .frcmod file as well.
Cheers,
Parker
On Tue, Jun 25, 2013 at 7:57 PM, Mark Abraham
hello:
I am using the command:
acpype.py -p prmtop -x S13.rst
to convert Amber system into Gromacs system, but it failed when I try to
generate .tpr file:
WARNING 1 [file prmtop_GMX.top, line 19]:
Too few parameters on line (source file toppush.c, line 300)
WARNING 2 [file
On Sun, Dec 9, 2012 at 9:46 AM, Albert mailmd2...@gmail.com wrote:
hello:
I am using the command:
acpype.py -p prmtop -x S13.rst
to convert Amber system into Gromacs system, but it failed when I try to
generate .tpr file:
WARNING 1 [file prmtop_GMX.top, line 19]:
Too few parameters
Have a good look in acpype, specially its wiki. There you'll see that acpype
is totally new code and among other things it covers amb2gmx.pl and solves
several of its drawbacks. It's not perfect though but for a system created
in tleap, the project is likely to be completed converted to gmx.
Alan
On 23/12/2010 6:02 PM, gromacs564 wrote:
Hi ,
I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam
web(they are glycam06 force field,included in AMBER) ,but cannot converted
this amber files to gromacs files format.
Can anyone help me to convert this
Have a look at acpype.googlecode.com
Alan
2010/12/23 gromacs564 gromacs...@126.com
Hi ,
I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam
web(they are glycam06 force field,included in AMBER) , but cannot converted
this amber files to gromacs files format.
Hi,
Not sure exactly what you plan to simulate but here are a couple of
potential pitfalls:
Does acpype call amb2gmx.pl or is it new code that converts? If it is a
amb2gmx.pl call I'd check the torsions on the NAc group if you have one.
They didn't get translated when I used it.
When using
Hi ,
I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam
web(they are glycam06 force field,included in AMBER) , but cannot converted
this amber files to gromacs files format. Can anyone help me to convert
this (amber) files to gromacs input files(top or
Hi, I am running a simulation of a protein DNA complex, and for this i
am using AMBER99 forcefield. The problem is that every complex I need
to run, I have to rename several residues and atoms, especially
hydrogen atoms one by one (well, actually using replace tool). And
this takes hours to get
Ragnarok sdf wrote:
Hi, I am running a simulation of a protein DNA complex, and for this i
am using AMBER99 forcefield. The problem is that every complex I need
to run, I have to rename several residues and atoms, especially
hydrogen atoms one by one (well, actually using replace tool). And
write some short PERL
script to do
the renaming for you.
Good Luck,
-Shay Amram
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Ragnarok sdf
Sent: Sunday, August 10, 2008 19:05 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] AMBER and gromacs atoms
-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Ragnarok sdf
Sent: Sunday, August 10, 2008 19:05 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] AMBER and gromacs atoms renaming
Hi, I am running a simulation of a protein DNA complex, and for this i
am using AMBER99
Dear all,
I hvae used ANTECHAMBER GAFF of Amber generate a .prmtop and .prmcrd
of
a small molecular(XK263, a inhibitor of HIV-1 PR). I want to use ffamber99 in
Gromacs-3.3.1 to do a simulation of it, but I can't get the force field of the
molecular used in Gromacs.
On the
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