- Original Message -
From: Yao Yao ya...@ymail.com
Date: Saturday, September 11, 2010 10:00
Subject: [gmx-users] OWT5 not found in Charmmff
To: gmx-users@gromacs.org
I am running tip5p in charmm force field in gmx. In energy
minimization step, it gives an error msg as below. I
Hi Alan,
I assume this is still the same issue on the same issue (same
machine/os) as you reported last time.
Could you provide some details about the version of OS, compiler,
CUDA, OpenMM you're using?
I'll look into the problem and get back to you if I figure out something.
Cheers,
--
OpenSuSE 11.2 on 64bit AMD computer.
Compiling and installation went smoothly without any warning or error messages.
However, when I attempted running gmxdemo, the execution hund in pdb2gmx, the
output file is attached.
Any help will be much appreciated.
Thanks in advance.
--
Stephen P.
On 2010-09-12 16.17, Stephen P. Molnar wrote:
OpenSuSE 11.2 on 64bit AMD computer.
Compiling and installation went smoothly without any warning or error messages.
However, when I attempted running gmxdemo, the execution hund in pdb2gmx, the
output file is attached.
Any help will be much
Hi GMX users,
I would like to perform MD with new developped CHARMM parameters in GROMACS.
Since these parameters are new, they are not presents in the ffcharm*.itp files
given in the of charmm27.ff in the latest GMX distribution. So I have already
made the conversions for the bonded
Dear all,
I have two question:
1) Are the atom types I chose for the use of OPLS force field correct?
I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate enzyme
drug interaction. Since the Dundee Prodrg Server converts PDB files of drug
structures just in an .itp file
Meyer-Almes, Franz-Josef, Prof. Dr. wrote:
Dear all,
I have two question:
1) Are the atom types I chose for the use of OPLS force field correct?
I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate
enzyme drug interaction. Since the Dundee Prodrg Server
I'm new to gmx so I'm just seeing if I'm able to make homoblock polypeptides.
I would like to simulate a 5 residue polyglycine. I've used PRODRG to generate
the pdb file, however trying to convert the file with pdb2gmx I receive the
error:
Fatal error:
Residue 'Y' not found in residue
On 2010-09-12 21.13, C Johnson wrote:
I'm new to gmx so I'm just seeing if I'm able to make homoblock
polypeptides. I would like to simulate a 5 residue polyglycine. I've
used PRODRG to generate the pdb file, however trying to convert the file
with pdb2gmx I receive the error:
Fatal error:
Hi,
I will be very thankful if someone can share a sample pbs script for running
Gromacs-4.5.
Thanks!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
manoj singh wrote:
Hi,
I will be very thankful if someone can share a sample pbs script for
running Gromacs-4.5.
Contact your system admins. There are far too many variables for such a setup
for anyone here to send such information.
-Justin
Thanks!
--
Thanks for the reply!
I will be very thankful if you can send me whatever you have.
I will change that according to my system.
On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edu wrote:
manoj singh wrote:
Hi,
I will be very thankful if someone can share a sample pbs
manoj singh wrote:
Thanks for the reply!
I will be very thankful if you can send me whatever you have.
I will change that according to my system.
If you know enough to make changes, then you probably know enough to get up and
running. A Google search for example PBS script turns up
Thanks for reminding me the existence of Google.
It must be hard to copy and paste few lines of the PBS script than
advertising the Google.
On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalem...@vt.edu wrote:
manoj singh wrote:
Thanks for the reply!
I will be very thankful if you can
Google given a link to very good site in regard.
http://biowulf.nih.gov/apps/gromacs/
On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalem...@vt.edu wrote:
manoj singh wrote:
Thanks for the reply!
I will be very thankful if you can send me whatever you have.
I will change that
I guess your pdb file has been damaged by a text editor (Word?). PDB
files are fixed format, you can not add or remove spaces at will. You
could try clicking together a peptide in Pymol or so, or drop the prodrg
output in Notepad (if you're on Windows). On mac or linux it should be
C Johnson wrote:
I guess your pdb file has been damaged by a text editor (Word?). PDB
files are fixed format, you can not add or remove spaces at will. You
could try clicking together a peptide in Pymol or so, or drop the prodrg
output in Notepad (if you're on Windows). On mac or
Manoj,
to suggest that Justin is being lazy would be to ignore the hundreds,
possibly thousands, of helpful posts that he has made on the gromacs
mailing list to assist users like yourself free of charge.
In fact, Justin was probably helping you more than you have realized
by pointing
it must be hard to do your own research
On Sep 12, 2010, at 5:52 PM, manoj singh wrote:
Thanks for reminding me the existence of Google.
It must be hard to copy and paste few lines of the PBS script than
advertising the Google.
On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul
If you simple replace HETATM with ATOM, i.e.:
:1,$s/HETATM/ATOM/
you shift all columns left by two characters. This is probably why, instead
of
reading GLY, pdb2gmx is reading Y only. The proper replacement would be:
:1,$s/HETATM/ATOM /
Note the two trailing spaces after
- Original Message -
From: ABEL Stephane 175950 stephane.a...@cea.fr
Date: Monday, September 13, 2010 2:59
Subject: [gmx-users] charmm to gromacs nonbonded parameters after conversion
To: gmx-users@gromacs.org
Hi GMX users,
I would like to perform MD with new developped CHARMM
I apologize to all for this, as I meant it to be a single reply; but
as someone who has quietly watched the soon Dr. Lemkul bust his chops
providing first class advice/assistance to any and all, usually w/in
15 min, everyday for years, I could not abide someone suggesting less
than
:)
I am basically a Charmm and Amber user and I have used Gromacs 3.X coupe of
years ago. Now, for some reason I need to use Gromacs-4.x again. My old PBS
script is not working anymore for this newer version for Gromacs. I just
wanted to see if there is anything special required for the newer
- Original Message -
From: manoj singh mks.am...@gmail.com
Date: Monday, September 13, 2010 11:17
Subject: Re: [gmx-users] PBS script
To: Discussion list for GROMACS users gmx-users@gromacs.org
:)
I am basically a Charmm and Amber user and I have used Gromacs 3.X coupe of
years
Hi Chris,
Sorry if I have been rude is my response.
I am new to the Gromacs-4.0. I just thought if some one can not give
positive response to the query, that person should not be responding as this
prohibits the further response to the topic.
Again, thanks for your mail and sorry for my any
manoj singh wrote:
Hi Chris,
Sorry if I have been rude is my response.
I am new to the Gromacs-4.0. I just thought if some one can not give
positive response to the query, that person should not be responding as
this prohibits the further response to the topic.
There are no such rules
Justin,
Sorry if you felt insult.
I was having trouble running the gromacs at that point and therefore turned
to mailing in order to get some help. This topic seems to getting
unnecessary attention of many, which I certainly did not want.
I later found problem with mpdboot etc ( since this was
On 2010-09-13 00.06, C Johnson wrote:
I guess your pdb file has been damaged by a text editor (Word?). PDB
files are fixed format, you can not add or remove spaces at will. You
could try clicking together a peptide in Pymol or so, or drop the prodrg
output in Notepad (if you're on
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