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In continuation with my previous e-mail, I'm sorry to continue
bothering you with this but after reevaluating, it seems that problem
might just be with the amber forcefield after all as I manged to run
grompp just fine and to start the minimization by applying the OPLS
forcefield(with another OPLS compatible protein: bpti).<br>
I'm still interested in running my program with the amber forcefiled as
to be compatible with other calculations being done in the group. <br>
I would be most thankful for any suggestion you might have.<br>
<br>
Thanks a lot <br>
<br>
Arik<br>
<br>
On 4/24/2010 5:23 PM, Arik Cohen wrote:
<blockquote cite="mid:4BD38B6F.7020005@biochem.duke.edu" type="cite">
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Thanks again for the ultrafast response.<br>
<br>
1. The extra '.' is a typo. (I apologize for that). In the command the
file name appears as 1bgq_Complex_b4ion.tpr<br>
in addition, Both the single precision and double
precision(grompp_d) gives this error. <br>
The compilation was done with gcc-4.4.3 with and without the option
of --disable-float for the double and single precision version
respectively. <br>
<br>
2a. This is the first call to grompp<br>
<br>
b. The following programs such as pdb2gmx_d, editconf_d and genbox are
working properly.<br>
<br>
c.grompp/_d -h is working , giving a description on the program with
the different options available.<br>
<br>
3. With regards of running grompp with different forcefield<br>
<br>
<b>Apparently the problem is with the l-bfgs option in the em.mdp
file.
This is due to the fact that when changing the integrator option to
steep, the program runs fine </b><br>
<br>
I'm sorry but I just saw this now.<br>
<br>
The l-bfgs integrator was chosen since I need to do normal mode
analysis<br>
<br>
Thanks a lot<br>
<br>
Arik <br>
<br>
<br>
On 4/24/2010 2:26 PM, Justin A. Lemkul wrote:<br>
<blockquote cite="mid:4BD361F5.5060302@vt.edu" type="cite">I suppose
the next set of questions to ask would be: <br>
<br>
1. How was Gromacs compiled? What options were specified? <br>
2. Does every instance of grompp fail? Do other inputs work? What
does "grompp -h" do? <br>
3. Does grompp seg fault with totally different systems (different
force fields)? <br>
<br>
-Justin <br>
<br>
Arik Cohen wrote: <br>
<blockquote type="cite">Thank a lot for your very fast response !.
Here are the requested details: <br>
<br>
1. Version 4.07 is being used. <br>
<br>
2. Upgrading from version 4.04 to 4.07 doesn't help. <br>
<br>
3. The grompp command given is: <br>
<br>
grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top
-o 1bgq_Complex_b4ion..tpr <br>
<br>
4. em.mdp: <br>
<br>
integrator = l-bfgs <br>
nsteps = 50000 <br>
nstlist = 1 <br>
rlist = 1.0 <br>
coulombtype = PME <br>
rcoulomb = 1.0 <br>
vdw-type = cut-off <br>
rvdw = 1.0 <br>
nstenergy = 10 <br>
emtol = 5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0 <br>
define = -DFLEXIBLE ; using flexible water model <br>
<br>
<br>
5. The grompp command is issued in this case, before genion. However,
even when running it alone the same problem arises. <br>
<br>
6. The program is being run on Fedora 12 inside
VMware(2.6.32.11-99.fc12.i686, 32-bit). <br>
<br>
7. Running the same command on another OS and type of
machine(fc10.x86_64) does not solve the problem <br>
<br>
7. The output: <br>
<br>
:-) G R O M A C S (-: <br>
<br>
Gnomes, ROck Monsters And Chili Sauce <br>
<br>
:-) VERSION 4.0.7 (-: <br>
<br>
<br>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and
others. <br>
Copyright (c) 1991-2000, University of Groningen, The
Netherlands. <br>
Copyright (c) 2001-2008, The GROMACS development team, <br>
check out <a moz-do-not-send="true"
class="moz-txt-link-freetext" href="http://www.gromacs.org">http://www.gromacs.org</a>
for more information. <br>
<br>
This program is free software; you can redistribute it and/or <br>
modify it under the terms of the GNU General Public License <br>
as published by the Free Software Foundation; either version 2
<br>
of the License, or (at your option) any later version. <br>
<br>
:-) grompp_d (double precision) (-: <br>
<br>
Option Filename Type Description <br>
------------------------------------------------------------ <br>
-f MDP/em.mdp Input, Opt! grompp input file with MD parameters <br>
-po mdout.mdp Output grompp input file with MD parameters <br>
-c 1bgq_Complex_b4ion.pdb Input Structure file: gro g96 pdb
tpr tpb <br>
tpa <br>
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb
tpa <br>
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb
tpa <br>
-n index.ndx Input, Opt. Index file <br>
-p 1bgq_Complex.top Input Topology file <br>
-pp processed.top Output, Opt. Topology file <br>
-o 1bgq_Complex_b4ion..tpr Output Run input file: tpr tpb tpa <br>
-t traj.trr Input, Opt. Full precision trajectory: trr trj
cpt <br>
-e ener.edr Input, Opt. Energy file: edr ene <br>
<br>
Option Type Value Description <br>
------------------------------------------------------ <br>
-[no]h bool no Print help info and quit <br>
-nice int 0 Set the nicelevel <br>
-[no]v bool yes Be loud and noisy <br>
-time real -1 Take frame at or first after this time. <br>
-[no]rmvsbds bool yes Remove constant bonded interactions with
virtual <br>
sites <br>
-maxwarn int 0 Number of allowed warnings during input
processing <br>
-[no]zero bool no Set parameters for bonded interactions
without <br>
defaults to zero instead of generating an
error <br>
-[no]renum bool yes Renumber atomtypes and minimize number of <br>
atomtypes <br>
<br>
Ignoring obsolete mdp entry 'title' <br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# <br>
checking input for internal consistency... <br>
<br>
WARNING 1 [file MDP/em.mdp, line unknown]: <br>
For efficient BFGS minimization, use switch/shift/pme instead of
cut-off. <br>
<br>
processing topology... <br>
Opening library file
/usr/local/gromacs/share/gromacs/top//ffamber99sb.itp <br>
Opening library file
/usr/local/gromacs/share/gromacs/top//ffamber99sbnb.itp <br>
Opening library file
/usr/local/gromacs/share/gromacs/top//ffamber99sbbon.itp <br>
Segmentation fault (core dumped) <br>
<br>
<br>
Thanks a lot in advance for all your help <br>
<br>
Arik <br>
<br>
<br>
On 4/23/2010 4:45 PM, Mark Abraham wrote: <br>
<blockquote type="cite">On 24/04/2010 7:28 AM, Arik Cohen wrote: <br>
<blockquote type="cite">I'll be most thankful if any one would
be
able to help me with the <br>
following problem. <br>
</blockquote>
<br>
Giving more complete information will give you a much better chance.
It's not our job to be the family doctor and ask questions :-) <br>
<br>
What GROMACS version is it? Does upgrading to 4.0.7 help? <br>
<br>
<blockquote type="cite">While running the grompp (in both
single
and double precision) command I <br>
get a Segmentation fault (core dumped) error. <br>
</blockquote>
<br>
When? What was the output to date? <br>
<br>
<blockquote type="cite">The error persist even <br>
after recompiling the GROMACS with gcc-4.4.3(previously I was running <br>
4.04 compiled with the buggy gcc-4.1 compiler). <br>
</blockquote>
<br>
Does it happen on another machine? <br>
<br>
<blockquote type="cite">The command I'm using is: <br>
<br>
grompp_d -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
<br>
1bgq.tpr <br>
</blockquote>
<br>
What's in the .mdp file? <br>
<br>
Mark <br>
</blockquote>
</blockquote>
<br>
</blockquote>
</blockquote>
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