Hi,
I first simulated my protein system at 300 K. Now I want to simulate the
same protein system at high temperature (353.15 K). So, do I need to
perform the npt and nvt equilibration again at 353.1 K first and then the
final production run ?? Will it be okay to change the temp only in the
product
Thanks ..
On Wed, Jul 16, 2014 at 4:28 PM, rajat desikan
wrote:
> Hi,
> You need to perform the NVT and NPT equilibration at 353.1 K and then use
> your equilibrated system for the production run.
>
>
> On Wed, Jul 16, 2014 at 10:55 AM, bharat gupta
> wrote:
>
Hi,
I want to make an index file for a certain residue, say residue 14 and its
atom CA. I can eaily do that if its a single chain protein, but my protein
contains 10 chains and I don't know how to select residue 14 from each
chain. I tried splitting the protein into chains by using splitch option,
elects residue 14 in all chains in a multi chain protein. Hope that helps.
>
> Regards,
>
> On Wednesday, November 5, 2014, bharat gupta
> wrote:
>
> > Hi,
> >
> > I want to make an index file for a certain residue, say residue 14 and
> its
> > atom CA. I c
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>
> Hello,
>
> Can you index your residues so that each residue gets a unique number.
> pdb2gmx has an option "-renum" that will do this for you.
>
> Best,
> Eric
>
> On Tue, Nov
Hi,
My simulation stopped because of power outage and I restarted it using the
command:
mpirun -np 32 mdrun_mpi -cpi mdrun.cpt -s mdrun.cpt
It shows correctly the restarting time point, however the mdrun.log is not
getting updated and I don't know how to verify whether the simulation is
being co
Dear Gmx users,
I am performing a protein-ligand simulation using gromacs latest tutorial
for 5.0.x version. As per the tutorial, I included the coordinates of the
ligand in the complex.gro file (also updated total no. of atoms after
adding ligand atoms) and updated the topology file (topol.top) b
Dear Gmx users,
I am performing a protein-ligand simulation using gromacs latest tutorial
for 5.0.x version. As per the tutorial, I included the coordinates of the
ligand in the complex.gro file (also updated total no. of atoms after
adding ligand atoms) and updated the topology file (topol.top) b
metry and itp files for the ligand,
it's located far away from the active site. So, should I used the
unoptimized geometry coordinates in that case, but wouldn't it be wrong to
use the unoptimized geometry??
Thanks
--
BM
On Tue, Apr 19, 2016 at 10:08 PM, Justin Lemkul wrote:
>
>
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> | More info
> <http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=25130648872&tc_rand=1182875792&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_c
On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul wrote:
>
>
> On 4/19/16 9:01 PM, bharat gupta wrote:
>
>> Thanks for your prompt response.
>>
>> On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul wrote:
>>
>> [image: Boxbe] <https://www.boxbe.com/overvie
On Wed, Apr 20, 2016 at 10:10 AM, Justin Lemkul wrote:
>
>
> On 4/19/16 9:08 PM, bharat gupta wrote:
>
>> On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 4/19/16 9:01 PM, bharat gupta wrote:
>>>
>>> Thank
,
>
> If you mean you can not see the group with command `gmx make_ndx -f
> xxx.gro`, that's because you have not created one for it. Consult the
> manual for how to use make_ndx.
>
> Terry
>
Thanks Terry. I already discussed with Justin about this problem and now I
know
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>
>
>
> On
Dear Gmx Users,
I am interested in calculating cremer-pople parameters for a trisachharide
ligand from its simulation docked with a protein. I found one tool
g_puckering for calculating the parameters but it was written for Gromacs
version 4.0.x and I am using version 5.0.4. I am not able to compi
Dear GMX Users,
I am trying to perform QM/MM simulation for my system and I need to define
LA for the boundary between QM and MM region. I have the boundary regions
but I don't know how to add them in the gro file. Do I have to manually
modify the .gro file, if that's the case, adding, them manual
thod = am1
QMMMscheme = normal
QMbasis = sto-3g
QMcharge = 0
QMmult = 1
the QM parameters were copied from a tutorial (
http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html) to test the
trial run. I am using
; QMMM-grps= Protein_AS_5YWR
> QMmethod = am1
> QMMMscheme = normal
> QMbasis = sto-3g
> QMcharge = 0
> QMmult = 1
>
>
>
> the QM parameters were copied from a tutorial (
&g
Dear Gmx Users,
I am trying to run a QM-MM optimization using ORCA and Gromacs 5.1.2
version. I complied gromacs 5.1.2 with ORCA as QM-MM program. Here's the
output of CMakeCache.txt file for QM package:
//QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess,
// orca
GMX_QMMM_PROGRAM:
Dear Gromacs Users,
I am interested to know how to create a separate topology file for the QM
atoms of a system. It would be of great help if somebody can explain this.
For my QM system, I need to include the active site residues + ligand.
--
*Best Regards*
BM
--
Gromacs Users mailing list
*
Hi,
I have been trying to build the toplogy for cellopentoase using the newly
derived parameters mentioned in this paper:
http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the
gromacs website:
http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar
When I try to construc
Dear Gromacs Users,
I have been trying to simulate a docked complex of cellobiohydrolase with
cellotriose for the past 1 week. I have derived the parameters of
ellotriose from ATB server and with these parameters I am getting LINCS
warning at the nvt equilibration step, which I assume is due to th
Hello Gromacs Users,
I would like to know how to run the simulation on a cluster. I have cluster
in my lab with 6 nodes having 16 cpus and 4 nodes having 8 cpus. What
command do I have to use all the nodes? How do I know whether cpus from all
nodes are being used??
Thanks in advance for help
--
Hi,
How can I calculate the average number of salt bridges between two residues
during the entire simulation ??...
Thanks
---
Bharat
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Hi,
How can I calculate the average number of salt bridges between two residues
during the entire simulation ??...
Thanks
---
Bharat
--
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* Ple
Hi,
I want to calculate the average number of salt bridge interactions between
two residues. I used g_saltbr it gives the details for all the residues.
Using g_dist I calculated the distance between the charged group of those
two residues, but I want a number for salt-bridges like g_hbond gives ??
Thank you Justin... that's what I was looking for ...
On Tue, Nov 19, 2013 at 2:24 AM, Justin Lemkul wrote:
>
>
> On 11/14/13 10:18 PM, bharat gupta wrote:
>
>> Hi,
>>
>> How can I calculate the average number of salt bridges between two
>>
Hi,
I want to know whether is it possible to calculate solvation free energy of
protein in water using GROMACS. I came across a paper where they have done
the calculation using 3D RISM theory in AMBER...
Bharat
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Hi,
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has to be written in covar file .. According to manual it
says
-- Forwarded message --
From: bharat gupta
Date: Thu, Nov 21, 2013 at 4:52 PM
Subject: Re: Dihedral PCA
To: Discussion list for GROMACS users
Hi,
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index
Hi,
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has to be written in covar file .. According to manual it
says
Dear Gmx Users,
I extended a previously ran 10ns simulation by another 15ns by using the
following commands :-
tpbconv -s mdrun.tpr -extend 15000 -o next.tpr
mpirun -np 24 mdrun -s next.tpr -cpi mdrun.cpt -append -v
The number of frames for 10ns simulation were (5001) and when I checked the
exten
Thank you Mark and Chandan. I found two files traj.xtc and traj.trr that
were written for the extended simulation and I concatenated those
respective files with the previous trajectories.
Sorry to ask this here, but I have posted questions regarding PCA analysis
2 days back and I have not got any
HI,
Sorry for posting this question again on the forum
I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has t
If you have done the same mistake what I did, then you should get two files
with names traj.xtc and traj.trr. These files contains the results for the
restarted simulation. You can use trjconv to concatenate the new
(traj.xtc)+ previous(old.xtc) files. I hope this should work for you...
On Mon, D
Dear Vidya sankar,
I think this may help you with the REMD. Here's the link for the tutorial:
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3a_Mark_Abraham%2c_Session_1B
This tutorial deals with REMD and wa
Dear GMX Users,
I am trying to apply the REMD to study the difference between the folding
free energy of a 24 residue peptide with two different conformations. As I
am short of required number of processors for REMD in explicit water, I am
trying my luck with implicit solvent. I have come across
Dear GMX Users,
I am trying to apply the REMD to study the difference between the folding
free energy of a 24 residue peptide with two different conformations. As I
am short of required number of processors for REMD in explicit water, I am
trying my luck with implicit solvent. I have come across
Hi,
I have posted this query two times in the forum, but got no reply. Can
anybody give an advice on the following question ...
I am trying to apply the REMD to study the difference between the folding
free energy of a 24 residue peptide with two different conformations. As I
am short of requir
Hi,
I have some small doubt regarding using urea in simulation. Actually, I
calculated the the number of urea molecules for a particular concentration
in the box. For eg., the same box if filled with water occupies 43614
molecules of water and if I need to fill molecules of urea for 1M
concentrati
nd=89342066&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>|
> More
> info<http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=16530416634&tc_rand=89342066&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&am
Hi,
I am trying to add 5M urea in a box of volume 1453.73 cubic nm, which is
equal to 4377 molecules of urea. But while adding it using genbox command,
I get an error "killed" and the program stops after that. What is wrong
here, is my calculation correct or the size of box should need to be
incre
6066&tc_rand=680332635&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>
>
>
> On 3/5/14, 5:58 AM, bharat gupta wrote:
>
>> Hi,
>>
>> I am trying to add 5M urea in a box of volume 1453.73 cubic nm, which is
>> e
Hi,
I want to find the interacting hydrogen bonding residues with the residue
of my choice. I made an index for the residue for which I want to find the
hydrogen bonds and I get the number of hydrogen bond it makes during the
simulation. But how can I find the residue with which its making the
hyd
Hi,
I energy minimized a protein consisting 10 chains using gromacs. When I
converted the structure of the protein from gro format to pdb format to
visualize in Pymol, it shows only one chain in ribbon form and rest of the
chains are not shown ... How to rectify this error ??
Regards
-
Bhara
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> More
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>
>
>
> On 5/28/14, 9:24 PM, b
okay ,... thanks
On Thu, May 29, 2014 at 10:38 AM, Justin Lemkul wrote:
>
>
> On 5/28/14, 9:36 PM, bharat gupta wrote:
>
>> I am not concerned about secondary structure changes. But I want to
>> visualize the entire protein structure in ribbon form after energy
>&
that improves things. It
> always does for me.
>
> Chris.
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bharat
> gupta
> Sent: 28 May
nd#mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
Protein_chain_G 1
Protein_chain_H 1
Protein_chain_I 1
Protein_chain_J 1
SOL 288169
NA 144
On Thu, May 29, 2014 at
info<http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=17411327790&tc_rand=1534107469&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>
>
>
> On 5/28/14, 10:04 PM, bharat gupta wrote:
>
>>
useful help on a Pymol mailing
> list.
>
> Chris.
> ________
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bharat
> gupta
> Sent: 28 May 2014 21:24
> To: Discussion list
ke a bug. What GROMACS command and version produced it?
>
> Mark
> On May 29, 2014 6:40 AM, "bharat gupta" wrote:
>
> > Thanks you all for your responses. As far the chain name is concerned,
> that
> > can be worked out by a simple script. But I found another iss
ssign the secondary structure to a protein
> > in case pymol doesn't do so automatically, which happens e.g. for
> > multi-MODEL structures.
> >
> > Kind regards,
> > Erik
> >
> > On 29 May 2014, at 07:16, Mark Abraham wrote:
> >
> > > I
Hi,
While issuing the command g_kinetics, I got an error saying that "the
program should be complied with GNU scientific library. Please install the
library and reinstall Gromacs". Is there an option where I can compile only
this tool, as rest of the other gromacs tools are working fine.
Regards
Hi,
While issuing the command g_kinetics, I got an error saying that "the
program should be complied with GNU scientific library. Please install the
library and reinstall Gromacs". Is there an option where I can compile only
this tool, as rest of the other gromacs tools are working fine.
Regards
p;utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>
> Yes, you can just compile this tool, but you still need to configure a new
> GROMACS build to use libgsl before "make g_kinetics" can be useful.
>
> Mark
>
>
> On Sat, May 31, 2014 at 4:17 AM, bharat gupta
>
Hi,
I extended a crashed simulation using the command :
mpirun -np 24 mdrun -v -s mdrun.tpr -cpi mdrun.cpt
I just stopped the restarted simulation after some time and found that
mdrun.log was not updated, because log file and results obtained from
gmxcheck are different.
Here's the last informa
Hi,
I want to know the default cutoff distance g_saltbr tool uses in
identifying the salt-bridges..
Regards
--
Bharat
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