Hi Bruce,
Thanks for your reply. I am workin on RHEL with architecture x86_64. when i
searched for libm.* I got a few location, I tried "make: again after
exporting these location in LD_LIBRARY_PATH. but i am getting the same error
again. I think, i didn't downloaded the appropriate files for insta
If you donot make it, it is as good as breaking it...
Sharada
-- Original Message --
From: Venkat Reddy
To: Discussion list for GROMACS users
Date: Fri, 6 Mar 2009 11:31:57 +0530
Subject: Re: [gmx-users] How to break a disulfide bond ???
Hai !
with "pdb2gmx -ss", i can select the ss bonds. But af
Hai !
with "pdb2gmx -ss", i can select the ss bonds. But after that, how to break
a particular ss bond (not all).
Thank you
On Fri, Mar 6, 2009 at 11:01 AM, sharada wrote:
>
> pdb2gmx -h
>
> sharada
>
>
> *-- Original Message --*
> From: Venkat Reddy
> To: Discussion list for GROMACS use
pdb2gmx -h
sharada
-- Original Message --
From: Venkat Reddy
To: Discussion list for GROMACS users
Date: Fri, 6 Mar 2009 10:50:24 +0530
Subject: [gmx-users] How to break a disulfide bond ???
Hai Every one ! Is it possible to break a disulfide bridge using gromacs
?If so,Can anybody suggest
Hai Every one ! Is it possible to break a disulfide bridge using gromacs
?If so,Can anybody suggest me, how to do it???
Thanks for ur valuable time
With best wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
___
Lee Soin wrote:
Hello, all!
Can make_ndx generate indices only for heavy atoms or C-alpha atoms in a
specified range of residues? And how? Thanks!
Yes. Type "help" at the make_ndx prompt to see several useful examples of
syntax.
-Justin
--
SUN Li
Department of Physics
Nanjing Universi
Hello, all!
Can make_ndx generate indices only for heavy atoms or C-alpha atoms in a
specified range of residues? And how? Thanks!
--
SUN Li
Department of Physics
Nanjing University, China
___
gmx-users mailing listgmx-users@gromacs.org
http://www.g
Justin A. Lemkul wrote:
1. write a gro/pdb file of the model (can VMD do this?)
VMD will create an all-atom force structure.
*Edit* "all-atom structure." My brain got caught between all-atom force field
and structure...been one of those days.
-Justin
--
===
٩ wrote:
Dear Gromacs users
I'm sorry the topic is not so clear. I have run a atomic model for a few
times, and the system that I want to simulate is too large to run. Now I
have to build a coarse grained model of lipid bilayer. Is there anyone
who has the experience?
I've heard that one use
Dear Gromacs users
I'm sorry the topic is not so clear. I have run a atomic model for a few times,
and the system that I want to simulate is too large to run. Now I have to build
a coarse grained model of lipid bilayer. Is there anyone who has the experience?
I've heard that one user just success
Dear Gromacs users
I'm sorry the topic is not so clear. I have run a atomic model for a few times,
and the system that I want to simulate is too large to run. Now I have to build
a coarse grained model of lipid bilayer. Is there anyone who has the experience?
I've heard that one user just success
Hi Andy,
I did some work on molecular oxygen back in 2006. There have been a few
requests for molecular oxygen parameters so I decided to
dig them up. Here are the parameters that I used for that work. I leave it to you to read the relevant papers and decide if
these parameters are appropriate
Dear all,
I am trying to rebuild the alpha helix of one the chains
which got destroyed during the simulation. I found that we can do that
by distance restraints. So my question what is a better way of
distance restraints i.e should I restrain the hydrogen bonds of the
helix or any part
Andy Torres wrote:
Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on
myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got
the following
Fatal error:
Residue 'OXY' not found in residue topology database
I check the ff and I did not found the oxigen molec
Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on
myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the
following
Fatal error:
Residue 'OXY' not found in residue topology database
I check the ff and I did not found the oxigen molecule.
I saw that somebody
victor doss wrote:
Hello,
when I run grompp I get the following error message always. Whoever
has a correct fix to get rid of this error message and get the actual
result, Please suggest.
Thanking you
Dr. Victor A. Doss
processing topology...
Generated 332520 of the 332520 non-bonde
Hello,
when I run grompp I get the following error message
always. Whoever has a correct fix to get rid of this error message and
get the actual result, Please suggest.
Thanking you
Dr. Victor A. Doss
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Hello,
when I run grompp I get the following error message always. Whoever has a
correct fix to get rid of this error message and get the actual result, Please
suggest.
Thanking you
Dr. Victor A. Doss
_
The new Windows Live
Hi,
I guess you are not aware that you are using 128 cores and you ask for 32 cores
to do PME.
Using -npme 64 will probably result in a much higher performance, but you
should check
the information printed at the end of the log file. If you PME load is really
around 0.5, the real
PME load rati
Hello,
I have a problem in extending a MD simulation in Gromacs.
When I use 32 processors for the calculation, everything goes OK. The
simulation finishes well and I can extend it with tpbconv.
However, I would like to increase the number of processors used up to 64.
Using the same options for
>I can add this forcefield to GROMACS for modelling the system. Are there any
>guys in this maillist who did so.
Yeah, look at me :)
>Any hints would be thanked.
~ Chapter 5 of the tutorial as Justin often says here...
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv
drugdesign wrote:
Dear GROMACS users,
I've got a warning during equilibration molecular dynamics with TIP3P solvent
(amber03 force field):
Warning: 1-4 interaction between 2 and 21 at distance 5.887 which is larger
than the 1-4 table size 2.000 nm
This usually means your system is exploding
drugdesign wrote:
Dear gromacs users,
I am using genion command to add ions to .tpr file which
was made for protein by use of amber03 force field.
In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx.
PDB format dictates 3 ch
Dear GROMACS users,
I've got a warning during equilibration molecular dynamics with TIP3P solvent
(amber03 force field):
Warning: 1-4 interaction between 2 and 21 at distance 5.887 which is larger
than the 1-4 table size 2.000 nm
This usually means your system is exploding,
if not, you should i
Dear gromacs users,
I am using genion command to add ions to .tpr file which
was made for protein by use of amber03 force field.
In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI,
which isnot recognized by next pdb2gmx.
This is not a big problem , but it looks is a l
Hi,
You mentioned it was from following a tutorial. In that case also
always check whether your line reads exactly the same as is stated in
the tutorial. Besides, indicate which tutorial, as there are many, and
if you find that it was an error in the tutorial rather than your
typo, also report tha
On Thursday, March 5, 2009 1:47:28 AM,
vivek sharma wrote:
> I am trying to Install topolbuild on my system, while doing so with
> the make file given in the topolbuild folder. but I end up with a list
> of error mentioned below:
> ..
> .
> .
> .
> .compare_FF.c:(.text+0x1285): undefined re
wuxiao wrote:
Hi,
I would like to perform some MD simulations for polymeric system using
GROMACS. Only to find that none of the existing force fields is suit to
my system. Fortunately, the force field functions and the coresponding
parametes have been published. So an idea comes to me that
Hi,
I would like to perform some MD simulations for polymeric system using
GROMACS. Only to find that none of the existing force fields is suit to my
system. Fortunately, the force field functions and the coresponding parametes
have been published. So an idea comes to me that whether I can a
Hi,
Please read the manual before posting a question.
g_cover -h will give you the answer.
Berk
> Date: Thu, 5 Mar 2009 15:57:39 +0800
> From: li.d...@gmail.com
> To: gmx-users@gromacs.org
> CC: li.d...@gmail.com
> Subject: [gmx-users] eigenvec.trr and eigenval.xvg
>
> Dear all,
>
> I us
Ms. Aswathy S wrote:
Ms. Aswathy S wrote:
Dear Gromacs users,
I am doing the MD of protein ligand complex. When I did the energy minimization
of this complex, in the result , the ligand molceule is moving far away from
the protein.
What could be the possible reason? can anyone tell me ho
Am 05.03.2009 um 07:44 schrieb Dechang Li:
Not sure about VMD, but you can write a short script for pymol in
python:
1: reading velocities from gro
2: converting gro2pdb
3: read in pdb into pymol
4: create cgo object containing arrow (search in the list archives or
on the wiki page of pymo
Ms. Aswathy S wrote:
> Dear Gromacs users,
>
> I am doing the MD of protein ligand complex. When I did the energy
> minimization of this complex, in the result , the ligand molceule is moving
> far away from the protein.
>
> What could be the possible reason? can anyone tell me how can i over
Hi,
error b sounds like a bug (not necessary in Gromacs though - could
also be compiler or MPI lib). The count should not be negative. May be
the integer which holds the count wraps? Do you get a core file when
the job crashes?
I might be enough to put
ulimit -c unlimited
in your jobscript to get
Hello, gmx users
I've been doing SMD with gromacs program. being a new user, i have some
questions.
I want to pull a small oragnic compound throught a cyclic peptide nanotube
which was inserted in the bilayer.
1. As some papers mentioned that the velocity is very important, what
velocity should i
Hi Flo,
Yes, I remember our talk about this problem about a year ago.
So what should be the correct notation now?
I just tried
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx
or
g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
and then g_analyze -integrate -f vac.xvg
but they give me a
36 matches
Mail list logo
