protein fromtrrfile
Siavoush Dastmalchi wrote:
> Dear Mark,
>
> Many thanks for your kind suggestion. I did all sorts of things as you
> suggested, however still I get the same error. Here are the commands that I
> use (I used grompp also to generate different tpr files):
&g
tract energies for protein fromtrr
file
Siavoush Dastmalchi wrote:
> Dear list,
>
> I am trying to extract energy profile for a protein molecule using rerun
> program from trajectory obtained by MD of protein solvated in a water box. I
> have created index file and reedited t
Dear list,
I am trying to extract energy profile for a protein molecule using rerun
program from trajectory obtained by MD of protein solvated in a water box. I
have created index file and reedited the original mdp file (removed the SOLs
from it) to get a new tpr file using grompp. I have extra
Hi,
You may try "tpbconv". Read help for "tpbconv" first.
Siavoush
From: [EMAIL PROTECTED] on behalf of Anamika Awasthi
Sent: Thu 2008/03/20 08:14 ق.ظ
To: gmx-users@gromacs.org
Subject: [gmx-users] wants to simulate for more timesteps
Dear Gromacs Users,
I h
x27;Makefile' line 417: syntax error
*** Error code 1 (bu21)
typically means you've edited the makefile manually, or moved the
source. Try a "make distclean" and start over from scratch with ./
configure!
Cheers,
Erik
On Mar 16, 2008, at 3:16 PM, Siavoush Dastmalchi w
David van der Spoel
Sent: Sun 2008/03/16 05:07 ب.ظ
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Siavoush Dastmalchi wrote:
> Hi,
> As I mentioned before, the installation stopped with the error shown below.
> Looking for your kind attentions.
de 1 (bu21)
From: [EMAIL PROTECTED] on behalf of Siavoush Dastmalchi
Sent: Sun 2008/03/16 03:44 ب.ظ
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] SGI installation problem
Hi,
I did the following changes and it seems that problem has been fixed. But, then
again I got the error saying th
; ^
>
> 3 errors detected in the compilation of "make_edi.c".
> *** Error code 2 (bu21)
> *** Error code 1 (bu21)
> *** Error code 1 (bu21)
>
>
>
>
> From: [EMAIL PROTECTED] on behalf of David van der Spoel
> Sent: Sun 2008/03/16 11:30 ق.ظ
on behalf of David van der Spoel
Sent: Sun 2008/03/16 11:30 ق.ظ
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Siavoush Dastmalchi wrote:
> Hi,
>
> Thanks to David for his suggestion. Now I have the following error. It is a
> bit of shame tha
;iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Sat 2008/03/15 08:15 ب.ظ
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation prob
Hi there,
This is a bit funny that I am posting this problem again, but I am hopping that
I may find a solution. I recently down loaded gromacs-3.3.3 and was trying to
install it on my sgi computer. I get error massage (as shown below). It seems
that many others also had such a problem, so won
Hi there,
This may not be relevant to this list but I am hopping to get an answer. The
problem is that I can't download the source code for Grommacs from the download
site and it seems that the link to web interface to the ftp server is not
working as well.
I tried to use an ftp program to con
Hi again,
The genion doesn't work. I issue the following:
$ genion -s fullmd.tpr -random -nname Cl -nn 8 -o out.gro -p test.top -g
genion.log
and get the error massage of:
Processing topology
---
Program genion, VERSION 3.3.1
Source code
Hi,
I don't know why I get the following error message when I use more than one
node when I run grompp (e.g., grompp -np 32 .). From previous emails, I
gathered that I need to reduce the number of nodes. But for me it just works
when I use a single node.
Any suggestions? Cheers, Siavoush
Hi Justin,
Many thanks for the advice.
Cheers, Siavoush
From: [EMAIL PROTECTED] on behalf of Justin A. Lemkul
Sent: Wed 2008/02/20 07:20 ب.ظ
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] unfolding a protein
Quoting Siavoush Dastmalchi
Siavoush Dastmalchi <[EMAIL PROTECTED]>:
> Hi there,
>
>
>
> I want to unfold a protein (hen egg white lysozyme) which has got 4 disulfide
> bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form
> and it didn't unfold. I know it may need long
Hi there,
I want to unfold a protein (hen egg white lysozyme) which has got 4 disulfide
bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form and
it didn't unfold. I know it may need longer time, but it doesn't show any sign
of even starting to unfold. I think I am restr
Hi There,
I know this is not related to GMX, but was wondering if any one has any
experience with mpi enabled zdock on linux based cluster. Specifically, I am
trying to use zdock2.3_linux_mpi version on a cluster of Opteron 2212 CPUs. It
looks like the application works on all nods but can not
Dear Mr Jahanbakhsh,
Hope that every thing is going okay with your works. While you are trying
different avenues to increase the performance of the cluster (by the way
what is the name of cluster?) I was wondering if you could kindly download
the MODELLER program from the following site and in
Hi there,
I know this is not related to GMX but was wondering if you could kindly help me
out to find a program for flexible alignment of molecules. I know GASP from
Tripos but will appreciate it if you could introduce to me others programs
available out there either commercial or freewares.
B
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