Dear gmx users,
My system is composed of a protein and water. I am working with CHARMM36.
For NVT equilibration , I get this error:
Software inconsistency error:
Some interactions seem to be assigned multiple times
I thought that somewhere in the system might have high energy, then it's
Hi Justin,
thank you for your mail.
Sorry that I didn't first check than help.
Eva
On 7/11/12 10:24 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I wanted to ask if there is a possibility to tell pdb2gmx which residues
I
want to be protonated or not.
So that I can
I have another question about the option -ter of the pdb2gmx command.
I choose it because I thought that this is a way that I can determine what
shell happen with the termini but I was not ask anything by the program.
My aim is it to block the termini with a neutral group. Is there a way to
do
Dear Gromacs users,
I was running the saltbridge calculations for a dimeric
protein simulation using g_saltbr, But its taking very
long time, almost four days still its not completed.
Could anyone has suggestion regarding this issue? I am
using the same system -
Intel(R) Core(TM) i7-2600 CPU @
Hi Justin,
Thanks for the effort to help me.
I still no out of the error. The following is the content of my
topol_popc.top
; Include chain topologies
#include gromos53a6_lipid.ff/forcefield.itp
#include popc.itp
; Include water topology
#include gromos53a6_lipid.ff/spc.itp
; Include ion
Hi everybody,
I want to cap the terminal groups of my protein. I thought that I could
use the command pdb2gmx -ter. But when I use it nothing happens.
I am not ask anything so I could not choose none.
But when I just write pdb2gmx -ter none the following error comes up:
Invalid command line
On 7/12/12 1:42 AM, tarak karmakar wrote:
Dear All,
I am simulating a protein in gromacs with amber force field. The
protein shows maximum biological activity at pH 5.0 and at pH 7.4 it
shows no activity. So whichever biological process I am going to model
should be at the biologically
On 7/12/12 4:37 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
I have another question about the option -ter of the pdb2gmx command.
I choose it because I thought that this is a way that I can determine what
shell happen with the termini but I was not ask anything by the program.
My
On 7/12/12 4:51 AM, Kavyashree M wrote:
Dear Gromacs users,
I was running the saltbridge calculations for a dimeric
protein simulation using g_saltbr, But its taking very
long time, almost four days still its not completed.
Could anyone has suggestion regarding this issue? I am
using the same
Hi Justin,
so you mean that I first have to add the capping groups to my structure
and then run pdb2gmx with the -ter function?
But how can I add the capping groups to the structure?
On 7/12/12 4:37 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
I have another question about the
On 7/12/12 4:59 AM, J Peterson wrote:
Hi Justin,
Thanks for the effort to help me.
I still no out of the error. The following is the content of my
topol_popc.top
; Include chain topologies
#include gromos53a6_lipid.ff/forcefield.itp
#include popc.itp
; Include water topology
#include
On 7/12/12 6:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
so you mean that I first have to add the capping groups to my structure
and then run pdb2gmx with the -ter function?
Yes. The capping groups (see your force field's .rtp file for available
entries) are
Dear Sir,
That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95% since long and CPU usage drops down to 1.5 -2 %
but in many cases i have seen that still it will run (off course
slowly) and finish. But this was too long. So any
On 7/12/12 6:38 AM, Kavyashree M wrote:
Dear Sir,
That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95% since long and CPU usage drops down to 1.5 -2 %
but in many cases i have seen that still it will run (off course
slowly) and
Thanks :). will check whether it makes it faster.
On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 6:38 AM, Kavyashree M wrote:
Dear Sir,
That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95%
Dear Gromacs,
Is there really no other way to get the potential energy of the system
more accurately (6 digits)
than compiling in double precision?
Gromacs is giving eight digits after an succesfull cg minimization
even when compiled with single precision.
Eight digits would be enough for me.
Hi all,
I have an protein and drg complex. I've done the MD in SPC water
environment. Now I would like to check number of hydrogen bond formed
between the drug and protein, water as well. What will the right command for
me to analyse. Thanks in advance
--
View this message in context:
On 7/12/12 8:02 AM, Raj wrote:
Hi all,
I have an protein and drg complex. I've done the MD in SPC water
environment. Now I would like to check number of hydrogen bond formed
between the drug and protein, water as well. What will the right command for
me to analyse. Thanks in advance
Dear Sir,
I had a problem again during g_saltbr calculation it needs
.xtc and .tpr file, I can reduce the .xtc file to have only
protein but .tpr file will have water also in it. inorder to generate
new tpr file without water using grompp, i need topology file
without water .. so do you suggest
On 7/12/12 8:15 AM, Kavyashree M wrote:
Dear Sir,
I had a problem again during g_saltbr calculation it needs
.xtc and .tpr file, I can reduce the .xtc file to have only
protein but .tpr file will have water also in it. inorder to generate
new tpr file without water using grompp, i need
On 2012-07-12 14:01, Markus Kaukonen wrote:
Dear Gromacs,
Is there really no other way to get the potential energy of the system
more accurately (6 digits)
than compiling in double precision?
Gromacs is giving eight digits after an succesfull cg minimization
even when compiled with single
I read that. but while executing tpbconv i did
not see where i can specify that i do not want
solvent?
Thanks
Kavya
On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 8:15 AM, Kavyashree M wrote:
Dear Sir,
I had a problem again during g_saltbr calculation
Ok may be i need to specify an index file. I will try that.
And regarding the WARNING: this .tpx file is not fully functional.
I hope it will work fine enough to finish g_saltbr calculation?
Thanks
Kavya
On Thu, Jul 12, 2012 at 5:59 PM, Kavyashree M hmkv...@gmail.com wrote:
I read that. but
On 7/12/12 8:31 AM, Kavyashree M wrote:
Ok may be i need to specify an index file. I will try that.
And regarding the WARNING: this .tpx file is not fully functional.
I hope it will work fine enough to finish g_saltbr calculation?
In principle, you should be prompted to choose a default
Dear Sir,
Thank you It worked :). a very usefull suggestion.
But it did not promt to choose any option. I used
index file.
Thank you
Kavya
On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 8:31 AM, Kavyashree M wrote:
Ok may be i need to specify an index
Hello all,
I m performing a pulling simulation on my Protein-Mg-GTP complex. I
have considered pulling between the GTP and a residue of protein.
The pull code in the .mdp file im using is as follows:
; Pull code
pull= umbrella
pull_geometry = distance ; simple distance increase
Can you please give me an example of such a modeling software?
I tried it with PYMOL but the results are not very good.
And I also found several programs but the are all not free.
Thank you,
Eva
On 7/12/12 6:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
so you mean
On 7/12/12 9:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Can you please give me an example of such a modeling software?
I tried it with PYMOL but the results are not very good.
And I also found several programs but the are all not free.
g_energy -dp IIRC.
g_energy -h is your friend. By the way in single precision you have 7-8 digits
only.
It seems that the X.edr file only contains 6 digits (if mdrun was done
with single precision).
So g_energy -f X.edr -dp gives me only 6 digits.
To wish list: X.edr file should contain as many
Dear Gromacs,
g_energy_d -f gromacs.edr -dp
does the trick, the information was in the output file, not in standard output.
THANK'S!
terveisin, Markus
On 12/07/2012, Markus Kaukonen markus.kauko...@iki.fi wrote:
g_energy -dp IIRC.
g_energy -h is your friend. By the way in single precision you
g_energy -dp IIRC.
g_energy -h is your friend. By the way in single precision you have 7-8 digits
only.
Unfortunately it seems that the X.edr file only contains 6 digits (if
mdrun was done with single precision).
So g_energy -f X.edr -dp gives me only 6 digits.
To wish list: X.edr file should
It could be possible tht you do not pull into the 'right' direction. if
there is another group between 'GTP' and 'Residue' you will get clashes
and 'Residue' won't move further (could be a water molecule, or some
other part of 'GTP').
If this happens you should observe an increase in the force
your pull force looks insanly high especially if your pulling a small piece of
residue? But for a whole protein of averidge 40 KDa, or 350 amino acids its
around 2000 to 3000 from liturature (only about 6 that I could find anyways).
I might thus be wrong, but wounder if you have a pull rate
On 7/12/12 3:43 PM, lloyd riggs wrote:
your pull force looks insanly high especially if your pulling a small piece
of residue? But for a whole protein of averidge 40 KDa, or 350 amino acids
its around 2000 to 3000 from liturature (only about 6 that I could find
anyways). I might thus be
Hi Justin,
Thanks for the suggestion I got it solved somehow. The main problem was in
the popc128b.pdb itself, it has first 64 lipids and half of the SOl
molecules followed by rest of the POPC and SOL molecules. When I rearranged
them the error was solved.
But now another thing I would like to
On 7/12/12 10:23 PM, J Peterson wrote:
Hi Justin,
Thanks for the suggestion I got it solved somehow. The main problem was in
the popc128b.pdb itself, it has first 64 lipids and half of the SOl
molecules followed by rest of the POPC and SOL molecules. When I rearranged
them the error was
Hi Justin,
I followed your comments and now at the stage of adding solvents.
I wonder to see the protein after shrinking step to have no SOL molecules as
there were SOL molecules in the source popc128b.pdb. Had we removed all the
original SOL molecules anywhere during the course of tutorial?
I
On 7/13/12 12:24 AM, J Peterson wrote:
Hi Justin,
I followed your comments and now at the stage of adding solvents.
I wonder to see the protein after shrinking step to have no SOL molecules as
there were SOL molecules in the source popc128b.pdb. Had we removed all the
original SOL molecules
Thanks for the comment. By the way how to make a bigger box at this time of
the tutorial without affecting any part of the system. Can I use editconf
with slightly bigger number for z-axis (something like 6.7 which was 5.7
before)?
Thanks
Peterson J
--
View this message in context:
39 matches
Mail list logo
