Hwankyu Lee wrote:
Dear GMX-users,
In "wheel" (helical projection tool), can I make colors for some
residues? Besides gray for hydrophobic residues, I also want to make
positive charged residues in blue, and negative charged residues in red.
Thank you for your help in advance.
Not without
Dear GMX-users,
In "wheel" (helical projection tool), can I make colors for some
residues? Besides gray for hydrophobic residues, I also want to make
positive charged residues in blue, and negative charged residues in red.
Thank you for your help in advance.
best,
Hwankyu.
_
for both popc and protein
> like
> below mentioned here?
> in " .top " file
> ; Include Position restraint file
> #ifdef POSRES
> #include "lip_posre.itp"
> #include "posre.itp"
> #endif
>
> or any other way to do position restrain for both.
Justin A. Lemkul wrote:
Quoting Mark Abraham <[EMAIL PROTECTED]>:
Justin A. Lemkul wrote:
The ffcharmmnb.itp file is incomplete, and I suspect ffcharmmbon.itp is
as
well.
Any idea what's going on?
No, since you haven't said why you think they're incomplete :-)
Sorry, I sent that a bit t
Quoting Mark Abraham <[EMAIL PROTECTED]>:
> Justin A. Lemkul wrote:
>
> >>> The ffcharmmnb.itp file is incomplete, and I suspect ffcharmmbon.itp is
> as
> >> well.
> >>> Any idea what's going on?
> >> No, since you haven't said why you think they're incomplete :-)
> >
> > Sorry, I sent that a bit
Justin A. Lemkul wrote:
The ffcharmmnb.itp file is incomplete, and I suspect ffcharmmbon.itp is as
well.
Any idea what's going on?
No, since you haven't said why you think they're incomplete :-)
Sorry, I sent that a bit too quickly, didn't I? I suspect ffcharmmnb.itp is
incomplete because
dear gmx users
Any rigorous approach available currently to solve the problems mentioned in
the link below ?
http://www.mail-archive.com/gmx-users@gromacs.org/msg03792.html
Is gromacs 4.0 going to have a way to deal with them ?
Sorry to bother if a solution has been posted already and I have mi
Quoting Mark Abraham <[EMAIL PROTECTED]>:
> Justin A. Lemkul wrote:
> > Thanks for the detailed and informative reply, Mark (as always). I have
> decided
> > there is probably something fundamentally wrong with what I've been doing.
> I've
> > been at this for several months, every time I get a f
Justin A. Lemkul wrote:
Thanks for the detailed and informative reply, Mark (as always). I have decided
there is probably something fundamentally wrong with what I've been doing. I've
been at this for several months, every time I get a few free minutes from my
main work, so I lost track of what
Thanks for the detailed and informative reply, Mark (as always). I have decided
there is probably something fundamentally wrong with what I've been doing. I've
been at this for several months, every time I get a few free minutes from my
main work, so I lost track of what I did at the very beginn
Justin A. Lemkul wrote:
Hi all,
As a number of others have attempted, I am exploring the use of the CHARMM force
fields in Gromacs. I have read about a number of difficulties throughout the
list archive, but I am seeing something that thusfar it seems no one has
reported, regarding nonbonded pa
Quoting [EMAIL PROTECTED]:
> hi all,
> i would like make MD simulation of heparin. the only files i have is the
> pdb file from protein data bank but residues in this file are unknown by
> gromacs. so i have to build the topology file. Is anyone had ever built
> topology files and parameters files
hi all,
i would like make MD simulation of heparin. the only files i have is the
pdb file from protein data bank but residues in this file are unknown by
gromacs. so i have to build the topology file. Is anyone had ever built
topology files and parameters files [or have any ideas] and could help in
Justin A. Lemkul wrote:
Hi all,
As a number of others have attempted, I am exploring the use of the CHARMM force
fields in Gromacs. I have read about a number of difficulties throughout the
list archive, but I am seeing something that thusfar it seems no one has
reported, regarding nonbonded pa
Hi all,
As a number of others have attempted, I am exploring the use of the CHARMM force
fields in Gromacs. I have read about a number of difficulties throughout the
list archive, but I am seeing something that thusfar it seems no one has
reported, regarding nonbonded parameters. Let me tell yo
On Feb 20, 2008, at 19:36 , [EMAIL PROTECTED] wrote:
Message: 4
Date: Wed, 20 Feb 2008 09:15:33 -0800
From: "Ilya Chorny" <[EMAIL PROTECTED]>
Subject: [gmx-users] T-Coupling and COM removal
To: "Discussion list for GROMACS users"
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain;
Quoting Subhrangshu Supakar <[EMAIL PROTECTED]>:
> Hi All !
> I want to do a MD study of a few molecules in a box of sodium cetyl
> sulphate.
> I want the the topology Sod-cetyl-sulphate with all its hydrogens as without
> that there would occur a mismatch
> in the number of atoms in the system an
Hi All !
I want to do a MD study of a few molecules in a box of sodium cetyl
sulphate.
I want the the topology Sod-cetyl-sulphate with all its hydrogens as without
that there would occur a mismatch
in the number of atoms in the system and the number of atoms in the topology
file. I tried the the du
Quoting sudheer babu <[EMAIL PROTECTED]>:
> Hi gmx users,
> I am trying to run position restrain step for protein embedded in popc. is
> it possible to do position restrain at a time for both popc and protein like
> below mentioned here?
> in " .top " file
> ; Include Position restraint file
> #if
Hi gmx users,
I am trying to run position restrain step for protein embedded in popc. is
it possible to do position restrain at a time for both popc and protein like
below mentioned here?
in " .top " file
; Include Position restraint file
#ifdef POSRES
#include "lip_posre.itp"
#include "posre.itp"
Quoting sudheer babu <[EMAIL PROTECTED]>:
> Dear gmx-users,
> I am working on membrane proteins, I have done position restrain step
> successfully but, I have doubt about that tc_grps how to use? I have
> searched in gmx-archives regrading this problem , but I found controversial
> answers like 1.
David, Berk,
> Hold on, if you are doing this with hardcore, there is a singularity
> in dG/dlambda. It won't be numerically integrable so whatever you
> compute will be in error. See my recent JCP paper that I referred you
> to before.
thats what I thought.
With the latest patched code, I get r
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
On Thu, 21 Feb 2008 14:54:35 +0530 (IST)
[EMAIL PROTECTED] wrote:
On Wed, 20 Feb 2008, Siavoush Dastmalchi wrote:
Hii!!
The time scale you have chosen is very less to see unfolding in proteins of
moderate length, because in such a short time u might be able to see just
local disturbances only,
On Wed, 20 Feb 2008, Siavoush Dastmalchi wrote:
Hii!!
The time scale you have chosen is very less to see unfolding in
proteins of moderate length, because in such a short time u might be able
to see just local disturbances only, even at temperature of 400K. You need to increase the
production r
Anirban Ghosh wrote:
Hi All,
Can anyone tell me how to take snapshots every 1 nano-sec of a 30
nano-se simulation? Which command should I use in GROMACS and how? Any
suggestion is welcome. Thanks
trjconv
Regards,
*Anirban Ghosh*
*M.Tech Bioinformatics*
*University of Hyderabad
*
Projec
Hi All,
Can anyone tell me how to take snapshots every 1 nano-sec of a 30 nano-se
simulation? Which command should I use in GROMACS and how? Any suggestion is
welcome. Thanks
Regards,
Anirban Ghosh
M.Tech Bioinformatics
University of Hyderabad
Project Trainee
Centre For DNA Fingerprin
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