Makoto Yoneya wrote:
Dear Mark and GMX users:
Mark wrote:
Where did cyggmx-4.dll come from? What build tools are you using?
No GROMACS distribution version of src/gmxlib/Makefile.in has such a
make target - I checked 3.3.1, 3.3.3 and 4.0.5. What conditions induced
its creation?
Could you
Kukol, Andreas wrote:
Many thanks for your help.
As for the 1-4 interactions, I am using the Gromos53a6 forcefield for
everything apart from this particular dihedral.
I did not exclude 1-4 interactions previously with the multiple dihedral terms.
Does this mean, if I use Ryckaert-Bellemans
Date: Fri, 29 May 2009 16:52:50 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] constant term in dihedral potential function
Kukol, Andreas wrote:
Many thanks for your help.
As for the 1-4 interactions, I am using the Gromos53a6 forcefield
Berk Hess wrote:
But this is a different issue.
These changes are to enable automatic parameter settings based on atomtypes
for multiple dihedrals over the same bonds.
Andreas specifies the parameters on the same line in the [ dihedrals ]
section.
In that case every works (and has alwats
Hi,
I have a 13 residue peptide which I have kept in a box using the following
command
editconf -f conf.gro -bt cubic -o box.gro -d 0.75
the flag -d 0.75 is given as per the ' minimum image
convention'.
When I solvate the box, 6772 water molecules get
sarbani chattopadhyay wrote:
Hi,
I have a 13 residue peptide which I have kept in a box using the
following command
editconf -f conf.gro -bt cubic -o box.gro -d 0.75
the flag -d 0.75 is given as per the ' minimum image convention'.
When I solvate the box, 6772 water molecules get added.
Dear Gromacs users,
I am currently working on Dynamic simulation studies using GROMACS software. In
my current work I want to do simulation of a protein containing Fe-S cluster.
If i directly do through pdb2gmx then it is giving a error massage like FES in
not included in .rtp file. Regarding
Hi All,
I am running Gromacs for drug enzyme complex using AMBER as
forcefield.While running pdb2gmx command I am getting error and warning of
790 missing atoms. Can anybody suggest me how to correct this error.
error :
---
WARNING: atom H
amri ta wrote:
Dear Gromacs users,
I am currently working on Dynamic simulation studies using GROMACS
software. In my current work I want to do simulation of a protein
containing Fe-S cluster. If i directly do through pdb2gmx then it is
giving a error massage like FES in not included in
It is not straightforward to use the AMBER forcefield with Gromacs. You need to
edit your pdb-file to account for different atom/residue names used by AMBER as
opposed to GROMOS forcefields.
Detailed info is here: http://chemistry.csulb.edu/ffamber/
If this is your first MD simulation, try
swa...@ncbs.res.in wrote:
Hi All,
I am running Gromacs for drug enzyme complex using AMBER as
forcefield.While running pdb2gmx command I am getting error and warning of
790 missing atoms. Can anybody suggest me how to correct this error.
Either supply a structure file that has suitable
hi i'm new to gromacs and want to simulate a protein inside a phospholipid
envelop (may be box or dodecahedron). for this i got the pdb files of both the
proteins and the lipids(e.g.POPC, POPE etc). but i'm facing a lot of problems
in generating the topology files as well as in running grompp
Samik Bhattacharya wrote:
hi i'm new to gromacs and want to simulate a protein inside a
phospholipid envelop (may be box or dodecahedron). for this i got the
pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but
i'm facing a lot of problems in generating the topology files
Thanx Justin...i must go throuh that tutorial. thanx for the help.
--- On Fri, 29/5/09, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] membrane protein simulation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Friday,
Hi Mark,
My *.mdp file:
cpp = /lib/cpp
integrator = md
;constraints = h-bonds
dt = 0.001
nsteps = 500
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstxtcout = 100
nstlog
osmair oliveira wrote:
Hi Mark,
My *.mdp file:
cpp = /lib/cpp
integrator = md
;constraints = h-bonds
dt = 0.001
nsteps = 500
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstxtcout
Dear Users,
We want to run gromacs molecular dynamics for a molecule which contains
the
following non standard amino acids: D-MeVal and L-Nva (norvaline) How
may we proceed to
parameterise these residues to include in the appropriate force field.
(ffG43a2.rtp). We would be grateful for any
On Friday, May 29, 2009 9:38:00 AM, vivek sharma viveksharma.i...@gmail.com
wrote:
Thanks a lot for your quick response. It is really encouraging to get
response from developers like you.
I tried generating topology again with the same command line and corrected
input file.This time
Hi :
Would anyone explain how to get the protein molecular weight from the
following note from the catalog?
mol wt single-chain mol wt 14.7 kDa
What does it mean single-chain?
Is it correct =
1 kDa = 1000 Da = MW 1000. So MW 240 = 0.24 kDa.
Thank you
Lin
Chih-Ying Lin wrote:
Hi :
Would anyone explain how to get the protein molecular weight from the
following note from the catalog?
mol wt single-chain mol wt 14.7 kDa
Where did this come from? Is this in the manual somewhere?
In any case it's probably just an example of expected output
david.lisgar...@canterbury.ac.uk wrote:
Dear Users,
We want to run gromacs molecular dynamics for a molecule which contains
the
following non standard amino acids: D-MeVal and L-Nva (norvaline) How
may we proceed to
parameterise these residues to include in the appropriate force field.
Please keep all correspondence on the gmx-users list. I do not advertise myself
as a private tutor :)
Shankar Prasad Kanaujia wrote:
Dear Justin,
I have done simulation of protein-ligand complex using gromacs v3.3.3.
The g_energy gives LJ-14, Coulomb-14, LJ-SR, Coulomb-SR energies,
however,
Shankar Prasad Kanaujia wrote:
Dear justin,
sorry for writing person mail.
I am attaching the .mdp file.
You are using a shift potential for vdwtype (and you haven't applied it
correctly - read the manual.) Therefore, LJ terms are cut off at rvdw (the LJ
term is zero beyond this point)
Dear gmx-users!
Hi,
I am trying to install an old version of Gromacs (gromacs-localp-3.0.2)
for local pressure calculation.
I successfully configured the gromacs with:
./configure –program-suffix=_d –prefix=/usr/local/gromacs333_double
–enable-double
...
farzaneh fatahi wrote:
Dear gmx-users!
Hi,
I am trying to install an old version of Gromacs (gromacs-localp-3.0.2)
for local pressure calculation.
I successfully configured the gromacs with:
./configure –program-suffix=_d –prefix=/usr/local/gromacs333_double
–enable-double
Perhaps you should
Hi
From the following website= it lists
Properties
grade for molecular biology
formlyophilized powder
mol wt single-chain mol wt 14.7 kDa
composition protein, ≥90%
storage temp. -20°C
How to get the molecular weight from the above protein properties?
L7651 Lysozyme from chicken egg
Hi
I want to simulate the system straight to 1ns.
How to print out .gro per 100 ps?
I only know Gromacs can print out the .gro file at the end of the simulation.
How can I print out the .gro in the middle way of simulation?
Thank you
Lin
___
Chih-Ying Lin wrote:
Hi
From the following website= it lists
Properties
grade for molecular biology
formlyophilized powder
mol wt single-chain mol wt 14.7 kDa
composition protein, ≥90%
storage temp. -20°C
How to get the molecular weight from the above protein properties?
This
Chih-Ying Lin wrote:
Hi
I want to simulate the system straight to 1ns.
How to print out .gro per 100 ps?
I only know Gromacs can print out the .gro file at the end of the simulation.
How can I print out the .gro in the middle way of simulation?
Have a look in the manual. Section 7.4 lists
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