On 2/15/13 4:00 PM, Abhishek Acharya wrote:
On 2/15/13 1:29 PM, Abhishek Acharya wrote:
Dear GROMACS Users.
Just out of curiosity, i would like to pose a general question here ( i
didn't have an idea of any other suitable forum ). My protein active
site
has a GDP which is coordinated to a
On 2/15/13 4:20 PM, 라지브간디 wrote:
Where can I change the particular Ligand atom ( can be C, O and N...etc)
non-bonded interaction value and charges ?
In its topology.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Hello!
I'm trying to diagonalize the matrix by using g_covar.
However my matrix is too large (5x5) so it won't diagonalize the
matrix.
Is there a different software or different command that I could try to use
in order to diagonalize my matrix as quickly as possible?
Thank you.
--
Where can I change the particular Ligand atom ( can be C, O and N...etc)
non-bonded interaction value and charges ?
--
gmx-users mailing listgmx-users@gromacs.org
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>
> On 2/15/13 1:29 PM, Abhishek Acharya wrote:
>> Dear GROMACS Users.
>> Just out of curiosity, i would like to pose a general question here ( i
>> didn't have an idea of any other suitable forum ). My protein active
>> site
>> has a GDP which is coordinated to a Mg ion. The Mg ion itself
>> co
On 2/15/13 3:22 PM, zugunder wrote:
Oh, forgot about it completely... Thank you very much!
BTW, is there any automated way to get rid of solvent molecules in PDB? I
just need the structure for further manipulations (like mutations and adding
several residues to the end). I do not find any opti
Oh, forgot about it completely... Thank you very much!
BTW, is there any automated way to get rid of solvent molecules in PDB? I
just need the structure for further manipulations (like mutations and adding
several residues to the end). I do not find any options in editconf,
deleting manually from
On 2/15/13 2:08 PM, zugunder wrote:
Hi,
I bumped into a small problem, I think I missed something... so I am asking
for help.
I made a simulation of a protein in water (35ns, extended 3 times from
initial 10ns) and now I need to get a resulting protein structure in pdb.
So I issued:
g_trjcon
On 2/15/13 1:29 PM, Abhishek Acharya wrote:
Dear GROMACS Users.
Just out of curiosity, i would like to pose a general question here ( i
didn't have an idea of any other suitable forum ). My protein active site
has a GDP which is coordinated to a Mg ion. The Mg ion itself coordinates
two water
Hi,
I bumped into a small problem, I think I missed something... so I am asking
for help.
I made a simulation of a protein in water (35ns, extended 3 times from
initial 10ns) and now I need to get a resulting protein structure in pdb.
So I issued:
g_trjconv -s md_input_extended_to35ns.tpr -f md_
Dear GROMACS Users.
Just out of curiosity, i would like to pose a general question here ( i
didn't have an idea of any other suitable forum ). My protein active site
has a GDP which is coordinated to a Mg ion. The Mg ion itself coordinates
two water molecules and is held in position via non-bonded
> Date: Wed, 13 Feb 2013 16:07:53 +
> From: Steven Neumann
> Subject: [gmx-users] Bond potential of atom groups
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Gmx Users,
>
> I want to create coarse grained model. I need
Dear all,
We have run of three temperatures simulation (unfolding) and three replicates
of them. we are interested to calculate the experimental errors.
anyone has idea how do it?
regards,
Ravi
--
gmx-users mailing listgmx-users@gromacs.org
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You can not use different index files.
You must use different groups in the same index. Merge the 2 ndx into one
single file.
Cheers
Nuno Azoia
On Fri, Feb 15, 2013 at 1:58 PM, 라지브간디 wrote:
> How do i use two different ndx file ( which has few residues) as a input
> to calculate between their d
How do i use two different ndx file ( which has few residues) as a input to
calculate between their distance using g_dist, g_mindist and so on?
Regards
Raju
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Dear Justin.
The errors have now gone away once I followed your suggestion of entering
the missing parameters directly in the topology file. Though there is no
explanation as to why it didn't work with ffbonded.itp, I guess sometimes
ignorance is bliss ;)
Thanks again.
Cheers
Abhishek
>
>
> On 2/
Hi Henri,
Have you been able to solve this problem?
Best,
Valentina
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gmx-use
I have VOTCa already installed. Thank you for this.
Steven
On Wed, Feb 13, 2013 at 10:34 PM, Broadbent, Richard
wrote:
> Dear Steven,
>
> There is no universal method to do this and many people spend years
> studying the various techniques. However,
> http://pubs.acs.org/doi/abs/10.1021/ct900369
On Thu, Feb 14, 2013 at 6:13 AM, 라지브간디 wrote:
> Dear gmx,
>
> I've used -pbc nojump options but still the protein goes all around the
> box within 4ns. Any specific command to avoid this ? It's a myoglobin
> protein!
>
The usual approach is here:
http://www.gromacs.org/Documentation/Terminology/
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