On 14/05/2012 2:24 PM, mohan maruthi sena wrote:
Hi all,
I want to define a potential form and give it as input for
which i have seen manual ,thought gromacs table option is fine, i have
an example of generating 9-6 potential form , My question is how to
generate table.xvg, what is
On 14/05/2012 3:52 PM, Anirban wrote:
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists
of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120
cores) using mpirun and gives proper
Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
get the dssp plot.
Thanks
bunty
--
On 14/05/2012 4:14 PM, bunty xy wrote:
Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
On Mon, May 14, 2012 at 11:35 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 14/05/2012 3:52 PM, Anirban wrote:
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
arounf 1,17,000
On 14/05/2012 4:18 PM, Anirban wrote:
On Mon, May 14, 2012 at 11:35 AM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote:
On 14/05/2012 3:52 PM, Anirban wrote:
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36
FF on
On 11/05/2012 6:43 PM, Marzinek, Jan wrote:
Dear Gmx Users,
Many of you probably faced an error:
An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: '20s'
As I noted this error comes from the changes in the
Hi,
You do not need to use the polarizable martini water model to calculate the
dipole of molecules. Or I am missing a point here!
g_dipole should do the work
XAvier.
On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote:
Dear Justin,
Thank you very much from your response.
Thanks for your suggestions.
Now, I think that it's better to add the N atom of next residue to the .pdb
file and then add hydrogen atoms to its .mol2 format. Because when I open
formyl.pdb in chimera software and add hydrogens to it, it becomes an
formaldehyde and then I get the a wrong
On 14/05/2012 6:00 PM, Shima Arasteh wrote:
Thanks for your suggestions.
Now, I think that it's better to add the N atom of next residue to
the .pdb file and then add hydrogen atoms to its .mol2 format. Because
when I open formyl.pdb in chimera software and add hydrogens to it,
it becomes
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Thanks for your suggestions.
This is the .itp file got from the SwissParam.
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 C=O 1 LIG C 1 0.5700 12.0110
2 O=C 1 LIG O 2 -0.5700 15.9994
3 NC=O 1 LIG N 3 -0.7301 14.0067
4 CR 1 LIG CA 4
Dear Gromacs users,
I'm new to molecular dynamics and I face some problems with the analysis of my
trajectories.
I intend to use the trjconv utility to extract frames from my trajectories. Each
trajectory can contain several frames that belong to different clusters. To do
this I create an .ndx
Thanks for your suggestions.
Now I got the .itp file for frmyl+valine(the next residue).
This is the .itp file got from the SwissParam.
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 C=O 1 LIG C 1 0.5700 12.0110
2 O=C 1 LIG O 2 -0.5700 15.9994
3 NC=O 1
Dear all gromacs users,
I tried the grompp and i got the following error.number of coordinates
in coordinate file (4INS_b4ion.gro, 90396)
does not match topology (4INS.top,
90393).
Is there any explanation why is this
Dear gmx-users, I have some doubts on the manual pages. Kindly help to
understand the same.
Section 5.7.1 Page 129
1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not present
in the pair list from normal Lennard-Jones parameters using fudgeLJ.
Is there any way that I can see/write
Dear Suryanarayana Seera
Please check the itp files mentioned in the topol.top and what u used in
your commands. Especially check the solvent model. May be you have not changed
that in the topol.top file.
From: gmx-users-boun...@gromacs.org
On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote:
Hi,
You do not need to use the polarizable martini water model to
calculate the dipole of molecules. Or I am missing a point here!
g_dipole should do the work
XAvier.
Hi,
I want to point to another problem. If you
On Mon, 2012-05-14 at 11:55 +0200, Bala subramanian wrote:
Dear gmx-users, I have some doubts on the manual pages. Kindly help to
understand the same.
Section 5.7.1 Page 129
1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not
present in the pair list from normal
Interesting ...
do you have a reference for this?
XAvier.
On May 14, 2012, at 12:01 PM, Dommert Florian wrote:
On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote:
Hi,
You do not need to use the polarizable martini water model to
calculate the dipole of molecules. Or I am missing a
On Mon, 2012-05-14 at 12:27 +0200, XAvier Periole wrote:
Interesting ...
do you have a reference for this?
Sure, a detailed discussion about charges for the liquid phase and
results for molecular ionic liquids are published in:
http://dx.doi.org/10.1039/C1FD00051A
and
Dear Gmx Users,
i run the implicit simulation with virtual sites on the hydrogen of my
protein. Now I want to extract coordinates and run another simulation (in
explicit solvent). Is there any way to remove those virtual sites from my
gro file as VMD write the file using atoms not recognized by
On 5/14/12 8:42 AM, Steven Neumann wrote:
Dear Gmx Users,
i run the implicit simulation with virtual sites on the hydrogen of my protein.
Now I want to extract coordinates and run another simulation (in explicit
solvent). Is there any way to remove those virtual sites from my gro file as VMD
On 14/05/2012 10:42 PM, Steven Neumann wrote:
Dear Gmx Users,
i run the implicit simulation with virtual sites on the hydrogen of my
protein. Now I want to extract coordinates and run another simulation
(in explicit solvent). Is there any way to remove those virtual sites
from my gro file as
On Mon, May 14, 2012 at 1:51 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 14/05/2012 10:42 PM, Steven Neumann wrote:
Dear Gmx Users,
i run the implicit simulation with virtual sites on the hydrogen of my
protein. Now I want to extract coordinates and run another simulation (in
Dear gmx users,
I made an .rtp file for formyl. First of all, how can I be sure that what I
built, is correct?
Sincerely,
Shima--
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Please search the archive at
Dear gmx users,
I changed the aminoacids.rtp file recently.
Now, when I run pdb2gmx, I get the fatal error:
atom H is missing in residue For 0 in the pdb file
You might need to add atom H to the hydrogen database of building
block For
in the file aminoacids.hdb
-Is it may as
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The
tpi.xvg files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4
On 5/14/12 10:43 AM, Shima Arasteh wrote:
Dear gmx users,
I made an .rtp file for formyl. First of all, how can I be sure that what I
built, is correct?
There are two levels of correctness. Level 1 is the syntactic correctness of
the .rtp entry itself, which can be verified with an
On 5/14/12 11:19 AM, Shima Arasteh wrote:
Dear gmx users,
I changed the aminoacids.rtp file recently.
Now, when I run pdb2gmx, I get the fatal error:
atom H is missing in residue For 0 in the pdb file
You might need to add atom H to the hydrogen database of building block For
in the file
Dear Users,
I am simulation bilayer composed of 81 DOPC and 21 cardiolipin (CL) in a
box size 6*6*20 (nm^3). For making this system I used DOPC system with a
zero surface tension and then I replaced each DOPC with one CL.
Now, I got strange result, after long run, some of lipid (most of them are
Hi Justin,
Thank you for the perl script. But I wonder now why there is a difference
between what shows in the hbmap.xpm file and the summary_HBmap.dat
generated.
For example, I found many occurrences of the second to last H-bond in the
20hbmap.xpm file attached (visualized by GIMP), but in the
Hello
I saw that in my force field parametrization I wrote the atom names and not the
atom types in the blocks like bonds, angles and so on.
Could this be a problem? Should I write the atom types in the blocks?
Greetings
Lara
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gmx-users mailing listgmx-users@gromacs.org
On 5/14/12 2:27 PM, Lara Bunte wrote:
Hello
I saw that in my force field parametrization I wrote the atom names and not the
atom types in the blocks like bonds, angles and so on.
In what file?
Could this be a problem? Should I write the atom types in the blocks?
That depends on the
Hi Justin
In my flamol.rtp file that I create in my force field order CHARMM27
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul jalem...@vt.edu
An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users
gmx-users@gromacs.org
CC:
Gesendet: 20:32 Montag,
On 5/14/12 2:34 PM, Lara Bunte wrote:
Hi Justin
In my flamol.rtp file that I create in my force field order CHARMM27
Atom names are correct in the .rtp file.
-Justin
--
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg,
Hi,
I am using freeze groups to hold the x, y, and z positions of specified
atoms fixed (to roughly simulate a fixed surface). I would like to keep the
positions of atoms of residuetypes AT1 and AT2 fixed. So, in my .mdp
file, I have the following keywords pertaining to freeze:
freezegrps =
Hello
I want to write my parameters in the ffbonded.itp file in the CHARMM27 force
field folder. I wrote my atom types in this file. This atom types are defined
by me in atomtypes.dat
grompp gives me an error
Fatal error:
Unknown bond_atomtype
for all my atom types. Do I have to declare
On 5/14/12 4:38 PM, Lara Bunte wrote:
Hello
I want to write my parameters in the ffbonded.itp file in the CHARMM27 force
field folder. I wrote my atom types in this file. This atom types are defined
by me in atomtypes.dat
There is no atomtypes.dat that is read by any Gromacs program, and
Hi
All needed parameters for [ angles ] in the topology are defined in my .rtp
file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This
still don't work. In the topology my [ angles ] block looks like
[ angles ]
; ai aj ak funct c0 c1
On 5/14/12 5:15 PM, Lara Bunte wrote:
Hi
All needed parameters for [ angles ] in the topology are defined in my .rtp
file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This
still don't work. In the topology my [ angles ] block looks like
[ angles ]
; aiajak
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