Dear users,
I have been trying to build la ligand topology of my ligand through the
PRODRG web server.
I have the following queries;
According to Justin's important tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
i am lost on how to allocat
Hi,
I am running membrane dynamics. After giving this commnad
> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
i am receiving the following errors:
Generated 837 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
tur
On 8/27/13 5:10 AM, MUSYOKA THOMMAS wrote:
Dear users,
I have been trying to build la ligand topology of my ligand through the
PRODRG web server.
I have the following queries;
According to Justin's important tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl
On 8/27/13 5:59 AM, sanjay choubey wrote:
Hi,
I am running membrane dynamics. After giving this commnad
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
i am receiving the following errors:
Generated 837 of the 2346 non-bonded parameter combinations
Excluding 3 bonded
Hi,
Is it possible to calc the PME on the CUDA card?
If it is possible, how can one do it?
Best,
grita
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Hi, a general question about writing molecule.rtp and how pdb2gmx treats it.
I have a few atom types and a few atoms per each atom type.
So a question - when I define interactions, say [ bonds ] can I define them
by atomtype, rather that atom number?!
*So like this:*
[ B31 ]
[ atoms ]
; atomn
No, that is not implemented. Roughly speaking, the CPU does the
PME+bondeds while the GPU does the short-ranged interactions. Moving
PME would only be worthwhile if there was a very weak CPU and it was
cheap to do any necessary communication between GPUs. That day is not
yet here :-)
Mark
On Tue,
On 8/27/13 12:30 PM, Valentina wrote:
Hi, a general question about writing molecule.rtp and how pdb2gmx treats it.
I have a few atom types and a few atoms per each atom type.
So a question - when I define interactions, say [ bonds ] can I define them
by atomtype, rather that atom number?!
*S
.rtp [bonds] requires atom names (because that's all that can be
reliably deduced from the coordinate file input)
.itp/.top [bonds] requires atom numbers (because prior sanity-ization
is assumed) to look up the atom types to look up the interaction
parameters
... and different force fields have sl
Ok, thank you!
I was hoping for an easier job.
My system is anyhow flying apart - trying to spot a problem. Hence trying.
One more question - [ pairs ] get automatically generated. But I don't need
1-4 LJ. So I can just remove them?
Thank you
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Dear Justin thank you for your Previous reply
I am following your methane/water free energy tutorial
I have Generated All .mdp files wiht Different LAMBDA value But When I Run job
using Your Job.sh script
in usr/local/gromacs4.6.2/bin I have Received the Following error ( I ma
running th
On Tue, Aug 27, 2013 at 7:05 PM, vidhya sankar wrote:
> Dear Justin thank you for your Previous reply
> I am following your methane/water free energy tutorial
> I have Generated All .mdp files wiht Different LAMBDA value But When I Run
> job using Your Job.sh script
> in usr/local/gromacs
Yes, can remove.
However, ability to remove don't depend on our desire,
but depend on Force field set of rules. If molecule
was parametrized with 1-4 LJ, it is not desirable to remove it.
If it is in-house force field which ignore 1-4 LJ, then one can
safely remove it.
Sergey
27.08.2013, 20:42
Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent
this output.
Thank you
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Hey :)
Sorry for replying a bit late. But the issues you mention in this and the
other posts are usually solved by closely reading the text of the tutorial,
not only the commands.
Cheers,
Tsjerk
On Sun, Aug 25, 2013 at 3:44 AM, The One And Only wrote:
> Never mind, I'm dumb. I just realized t
On 8/27/13 4:25 PM, Valentina wrote:
Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent
this output.
No, that's not how gen-pairs works. There are many excellent explanations of
how it works in the list archive, but suffice it to say it does not affect the
appearan
I've moved on from that point; now I'm stuck at where it asks me to remove
molecules of solvent from the topology file.
On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar wrote:
> Hey :)
>
> Sorry for replying a bit late. But the issues you mention in this and the
> other posts are usually solve
Hi ...,
You should have had a look at the topology file format in an earlier step.
At the end is a listing of molecules. As it says in the tutorial, you
replaced solvent by ions, and you have to make changes in the topology file
to match that replacement. Open the file in an editor, have a look ar
What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
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a text editor
On Tue, Aug 27, 2013 at 1:54 PM, The One And Only wrote:
> What kind of editor should I open it in? I have Pymol, but I don't know if
> it's the right one.
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> * Please search
An editor is a program to edit the text in a file: gedit, nano, vi, emacs,
... It'll be the equivalent of Windows' Notepad. Can you find a tutor
around to help you out with the basic usage of Linux? It's always difficult
to plunge into several different things at the same time, here 'using
linux',
My name is Ilea Graedel, and I work at Rescale (www.rescale.com), a
software company based in San Francisco, CA. Rescale provides a secure,
web-based platform for engineers, scientists, and researchers to perform
compute-intensive analyses in the cloud. We enable companies and academic
institutions
Hi!
I noticed that gromacs breaks molecules due to PBC during the output of
trajectories. I understand that this can be fixed with trjconv. Is there
any option in the parameter file to force gromacs to keep molecules whole?
If not is it for efficiency purposes?
Sorry, if this question might
On 8/27/13 8:02 PM, Gianluca Interlandi wrote:
Hi!
I noticed that gromacs breaks molecules due to PBC during the output of
trajectories. I understand that this can be fixed with trjconv. Is there any
option in the parameter file to force gromacs to keep molecules whole? If not is
it for effici
How important is it to do gentle heating (using simulated annealing) with
GBSA? Often with explicit water it is enough to perform some equilibration
with positional restraints. Would it be enough to do the same with
implicit solvent?
Thanks,
Gianluca
Dear Gmxers,
I want to simulate 5M nabr aqueous solution.To add the ions I use genion
command and add 22 na and br ions
respectively to the system of pure 108 water molecules.But on running the
command genion I get error message
Processing topology
Back Off! I just backed up topol.top to ./#top
Hi Deepak,
You have to set the minimal distance between ions lower. Check the help of
genion.
Cheers,
Tsjerk
On Aug 28, 2013 8:04 AM, "Deepak Ojha" wrote:
Dear Gmxers,
I want to simulate 5M nabr aqueous solution.To add the ions I use genion
command and add 22 na and br ions
respectively to t
Hi!
Just wondering whether gromacs has (or plans to implement) a correction
for the loss of long range LJ interactons? Something similar to
LJcorrection in NAMD or IPS in CHARMM.
Thanks!
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.
DispCorr might be what you are looking for, correction for LJ beyond the
cut-off.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
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