Hi Evelyne,
I haven't got a clue... But does it work if you use -settime when
concatenating the trajectories, to avoid having frames with the same time
index? It shouldn't cause a segfault, but it might.
Cheers,
Tsjerk
On Fri, Sep 6, 2013 at 7:20 AM, deplazes e.depla...@uq.edu.au wrote:
Hi
You're a genious. It works!
Thanks a lot
From: Tsjerk Wassenaar [via GROMACS]
ml-node+s5086n5011009...@n6.nabble.commailto:ml-node+s5086n5011009...@n6.nabble.com
Date: Fri, 6 Sep 2013 02:12:25 -0700
To: Evelyne Deplazes e.depla...@uq.edu.aumailto:e.depla...@uq.edu.au
Subject: Re: Segmentation
You also need to make a new index file that corresponds to the new , reduced
.tpr file
Cheers
E
Enjoy Ausserberg
From: Tsjerk Wassenaar [via GROMACS]
ml-node+s5086n5011009...@n6.nabble.commailto:ml-node+s5086n5011009...@n6.nabble.com
Date: Fri, 6 Sep 2013 02:12:25 -0700
To: Evelyne Deplazes
Hi Evelyne,
So I was reading carelessly... I didn't notice you used an index file with
trjcat. If you later try to use the same index file, that may indeed cause
a segfault. Good that it works now.
Cheers,
Tsjerk
On Fri, Sep 6, 2013 at 12:29 PM, deplazes e.depla...@uq.edu.au wrote:
You also
Dear users,
I have a dimeric protein system, where I would like to define two pairwise
sidechain-sidechain distances, one in each monomer. I'd like to do this
back and forth, so that I can alternately enforce long (~0.6nm) and short
(~0.3nm) distances, and follow the response of the protein. I
Hi guys,
My problem is in the first step itself.
Fatal error:
Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms
while sorting atoms.
I understand that the problem is with the .rtp database. But. My doubt
is how to create a new rtp entry for that missing residue.
The
On 9/6/13 8:52 AM, Santhosh Kumar Nagarajan wrote:
Hi guys,
My problem is in the first step itself.
Fatal error:
Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms
while sorting atoms.
I understand that the problem is with the .rtp database. But. My doubt
is how to
Dear Rafael,
Thanks for your reply.
Yes, I did follow the link. This means that the system is not equilibrated
well. I tried to perform some more minimization but it seems that steepest
decent have already minimized it well.
Therefore I decided to perform MD at lower T. I tried 5ns of NVT
If I use the topology and coordinates of a small molecule from ATB for
docking (structure.pdb / structure.itp which match in atom numbering and
sequence); after docking and saving the structure_dock.pdb, the atom
numbering does not match the numbering in the structure.itp file. This
causes
Hi,
I am trying to build itp file for polymer simulations using OPLS-AA and had
two questions I could not find a clear answer from the forum or the manual.
1. Is the order of bond types listed in a row of the [dihedral] section
important, i.e. if I replace ijkl by lkji, will this make any
Sorry ..,here are my distance restraints file:
[ distance_restraints ]
;ai ajtypeindextype'low
up1up2fac
3012679 1 0 1 0.0
1.62142.2111.0
3012696
On 9/6/13 5:23 PM, Rama wrote:
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy
NMR experimental data.
Without restraints there is no problem, but if I include distance restraints
in topology file, getting fatal error:
the lipid atom index # was not
Please don't reply to the entire digest; the archive is hopelessly confused as
it is, but let's not make it any worse ;)
On 9/6/13 2:29 PM, R R S Pissurlenkar wrote:
If I use the topology and coordinates of a small molecule from ATB for docking
(structure.pdb / structure.itp which match in
On 9/6/13 5:27 PM, Rama Krishna Koppisetti wrote:
Sorry ..,here are my distance restraints file:
Without context as to what these numbers are, there's little useful information
here. I suspect you're trying to implement restraints between protein and lipid
atoms, which will not work for
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy
NMR experimental data.
Without restraints there is no problem, but if I include distance restraints
in topology file, getting fatal error:
the lipid atom index # was not recognized by using this command:
g_grompp
On 9/6/13 2:11 PM, prateekj wrote:
Hi,
I am trying to build itp file for polymer simulations using OPLS-AA and had
two questions I could not find a clear answer from the forum or the manual.
1. Is the order of bond types listed in a row of the [dihedral] section
important, i.e. if I replace
H
i Justin,
Thanks for your reply.
How to do that?
On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:23 PM, Rama wrote:
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to
satisfy
NMR experimental data.
Without restraints there
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do that?
If .rtp entries exist for your lipid with the force field, it's simply a matter
of pdb2gmx -merge, choosing which chains should be written as a single
[moleculetype]. If the lipids are
On 9/6/13 5:56 PM, Rama Krishna Koppisetti wrote:
Hi Justin ,
Is there any script available in gromacs documentation or some where?
My guess is no. Ask Google.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of
Hi Justin ,
Is there any script available in gromacs documentation or some where?
Thanks
On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do that?
If .rtp entries
On 9/6/13 12:48 PM, Golshan Hejazi wrote:
Dear Rafael,
Thanks for your reply.
Yes, I did follow the link. This means that the system is not equilibrated
well. I tried to perform some more minimization but it seems that steepest
decent have already minimized it well.
Therefore I decided to
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