Dear All,
I am planning to perform a QM/MM calculation of my protein system. Can
anybody suggest me whether gromacs-4.5.5 can be patched with any latest
version of CPMD? If not, then please suggest me some combination of the
gromacs-cpmd versions.
I came across this tutorial, but there, both
Dear All,
I am planning to perform a QM/MM calculation of my protein system. Can
anybody suggest me whether gromacs-4.5.5 can be patched with any latest
version of CPMD? If not, then please suggest me some combination of the
gromacs-cpmd versions.
I came across this tutorial, but there, both
, Aug 1, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
On Thu, Aug 1, 2013 at 7:03 AM, tarak karmakar tarak20...@gmail.com
wrote:
Dear All,
Can anyone guide me how to perform the 'potential energy scan
Dear All,
Can anyone guide me how to perform the 'potential energy scan' for a
dihedral of a small molecule in gromacs?
Regrads,
Tarak
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
Dear All,
While simulating a protein, I see the rmsd fluctuates around a mean of 0.6
nm. I carefully looked at the trajectory (VMD movie) and saw there are two
flexible terminii fluctuating with a very high amplitude contributing to
the high value of RMSD. Is it ok to report this problem with
mark.j.abra...@gmail.comwrote:
Your call. Is that motion significant to what you are trying to report
by your observation of the RMSD?
Mark
On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar tarak20...@gmail.com
wrote:
Dear All,
While simulating a protein, I see the rmsd fluctuates
:
On 6/4/13 12:51 PM, tarak karmakar wrote:
Yeah!
It is indeed a silly point to generate a velocity distribution at 0 K. (
Maxwell-Boltzmann will be in trouble)
After the warm up, now let say my protein is in 300 K, can't I generate a
velocity distribution at 300 k (using the keyword gen_vel
Dear All,
Although I have set gen_temp = 300, it is showing the initial temperature
445.7 K, generated at the very beginning of the run.
gen_vel = yes ; velocity generation
gen_temp= 300
gen_seed= 93873959697
Is it because of a bad
is interacting with
certain residues.
So, then should I use these different velocity generating seeds during the
warm up step?
Thanks,
Tarak
On Tue, Jun 4, 2013 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/4/13 8:07 AM, tarak karmakar wrote:
Dear All,
Although I have set gen_temp
I'm extremely sorry for copying the other '.mdp' file here. This is the
modified one I just created after seeing your reply. In the previous case I
didn't use 'continuation'.
On Tue, Jun 4, 2013 at 9:47 PM, tarak karmakar tarak20...@gmail.com wrote:
Thanks Justin.
Sorry for not uploading
) during my production run?
Thanks,
Tarak
On Tue, Jun 4, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/4/13 12:17 PM, tarak karmakar wrote:
Thanks Justin.
Sorry for not uploading the full .mdp. Here it is,
; 7.3.3 Run Control
integrator = md
tinit
Dear All,
I have a little confusion with the non-bonding parameters conversion from
OPLS-AA to CHARMM in gromacs.
If I see the ffnonbonded.itp in both the cases I get the following numbers
OPLS-GROMACS
Sigma = 0.1644471 nm
Epsilon = (0.875044*4.184) = 3.66118 kJ/mol
All these parameters are for Mg2+, forgot to mention.
On Fri, May 31, 2013 at 10:48 PM, tarak karmakar tarak20...@gmail.comwrote:
Dear All,
I have a little confusion with the non-bonding parameters conversion from
OPLS-AA to CHARMM in gromacs.
If I see the ffnonbonded.itp in both
Dear All,
It seems the problem in the cut-off schemes while using charmm force
field in gromacs persists even in the latest gromacs-4.6.1 version.
Recently I have posted regarding this problem came in gromacs-4.5.5
version. If anybody has already tested this issue in the latest version,
Dear All,
How do I incorporate the 1-4 scaling factor ( e.g., 1.0 for CHARMM and
0.833 in AMBER) in gromacs? Or, is it internally taken care of by gromacs
while specifying the -ff flag?
NAMD input file uses the following keyword
1-4scaling 1.0 (for charmm force field)
Thanks,
, 2013 at 11:57 PM, tarak karmakar tarak20...@gmail.comwrote:
Oh !
Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp.
Restrains things I didn't follow properly, anyway I'll read about this.
On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/12/13 1
,
Tarak
On Fri, May 17, 2013 at 1:34 PM, tarak karmakar tarak20...@gmail.comwrote:
What about Dispersion Correction ?
But if I use this set of informations
; 7.3.3 Run Control
integrator = md; md integrator
tinit = 0 ; [ps
Dear All,
I'm using charmm force field for simulation of a protein ligand system.
I have read the paper implementation of charmm in gromacs by Bjelkmar,
JCTC'
They have used the following set up
coulombtype = PME
rcoulomb= 1.2
vdwtype = switch
rvdw
Dear All,
I'm using charmm force field for simulation of a protein ligand system.
I have read the paper implementation of charmm in gromacs by Bjelkmar,
JCTC'
They have used the following set up
coulombtype = PME
rcoulomb= 1.2
vdwtype = switch
rvdw
Dear All,
I'm using charmm force field for simulation of a protein ligand system.
I have read the paper implementation of charmm in gromacs by Bjelkmar,
JCTC'
They have used the following set up
coulombtype = PME
rcoulomb= 1.2
vdwtype = switch
rvdw
Dear All,
I'm using charmm force field for simulation of a protein ligand system.
I have read the paper implementation of charmm in gromacs by Bjelkmar,
JCTC'
They have used the following set up
coulombtype = PME
rcoulomb= 1.2
vdwtype = switch
rvdw
Dear All,
I'm using charmm force field for simulation of a protein ligand system.
I have read the paper implementation of charmm in gromacs by Bjelkmar,
JCTC'
They have used the following set up
coulombtype = PME
rcoulomb= 1.2
vdwtype = switch
rvdw
Dear All,
I'm using charmm force field for simulation of a protein ligand system.
I have read the paper implementation of charmm in gromacs by Bjelkmar,
JCTC'
They have used the following set up
coulombtype = PME
rcoulomb= 1.2
vdwtype = switch
rvdw
Dear All,
I have read the 'implementation of charmm in gromacs' by bjelkmar,
JCTC. There they have used following cut-offs
coulombtype=PME
rcoulomb=1.2
vdwtype=switch
rvdw=1.2
rvdw-switch=1.0
If I use the same numbers with rlist=1.2 it is showing warning saying
rlist should be at lear 0.1 - 0.3
I have read the 'implementation of charmm in gromacs' by bjelkmar,
JCTC. There they have used following cut-offs
coulombtype=PME
rcoulomb=1.2
vdwtype=switch
rvdw=1.2
rvdw-switch=1.0
I am not sure about rlist.
Regards,
Tarak
On Fri, May 17, 2013 at 1:46 PM, tarak karmakar tarak20...@gmail.com
...@eesti.ee
Tarak
-- Forwarded message --
From: tarak karmakar tarak20...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Date: Fri, 17 May 2013 15:50:25 +0530
Subject: Re: [gmx-users] Inconsistent results in different clusters and cores
On Fri, May 17
:42 PM, tarak karmakar tarak20...@gmail.com wrote:
I am extremely sorry for spaming the mail box. It was quite
unintentionally. Believe me I was getting the following error every
time while sending the mail.
Final-Recipient: rfc822; jaanus.k...@eesti.ee
Action: failed
Status: 5.0.0
Diagnostic
twice. Facing lot of problems,
here, in mail delivery failure.
Thanks,
Tarak
On Fri, May 17, 2013 at 6:22 PM, tarak karmakar tarak20...@gmail.com wrote:
@ Justin and Mark,
Do you have any idea about the rlist used by Bjelkmar et. al.
'Implementation of charmm in gromacs'? I see, they have
, tarak karmakar tarak20...@gmail.com
wrote:
Dear All,
I am running a simulation of ligand binding in a protein. Ligand is
mostly negatively charged, so as expected it should bind to the positive
region of the protein. To check the possible binding zone, I try to
calculate or rather
Dear All,
I am running a simulation of ligand binding in a protein. Ligand is
mostly negatively charged, so as expected it should bind to the positive
region of the protein. To check the possible binding zone, I try to
calculate or rather visualize the electrostatic potential map of a
Dear All,
I am simulating a protein in water to check the ligand movement over a
time span. I haveminimized the system in STEEP and CG and after that
heated from 0K - 300K within a time span of 300 ps. Then, I performed the
NPT production runs. In two clusters I have got different
:
On 5/12/13 1:17 PM, tarak karmakar wrote:
Dear All,
I am simulating a protein in water to check the ligand movement
over a
time span. I haveminimized the system in STEEP and CG and after that
heated from 0K - 300K within a time span of 300 ps. Then, I performed the
NPT
Remove all the hydrogens from the pdb file and then try to run pdb2gmx, I
hope it'll do fine.
Or you can also use -ignh option as suggested by Justin.
Tarak
On Fri, May 10, 2013 at 3:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/10/13 5:16 AM, Jernej Zidar wrote:
Hi,
In CHARMM I
lincs_warnangle = 30
On Sun, May 12, 2013 at 11:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/12/13 1:34 PM, tarak karmakar wrote:
Thanks Justin for the Quick and Helpful reply.
Yes. If I am right, the chaotic behavior of the simulations is
inherent
and can be assessed
Oh !
Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp.
Restrains things I didn't follow properly, anyway I'll read about this.
On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/12/13 1:53 PM, tarak karmakar wrote:
Thanks,
I have used CGENFF
/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials
it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph
Dear All,
During a simulation of a protein with a ligand, I see the -NH3 of the
lysine side chain near the ligand is getting squeezed for a very short
time; N-H bonds are getting contracted and the angle are no longer within
tetrahedral normal HNH angles. I have used LINCS to keep all the
Thanks Dr. Vitaly
Yeap !
From that point of view I'm seeing the correct temperature drift and
it reaches nicely to 300 K after say, 300ps.
But is it a good integrator ( SD ) to perform this job ? Or, should I
opt for other, like Lep-frog or MD-VV with let say , Berendsen
thermostat?
Please
Thanks Justin
Yah! We can run steered MD or Umbrella Pulling ( sampling) for this
purpose. But one thing I am wondering that how to move the entire
complex. In my model there are no covalent bond ( bonding info)
between the metal and ligands. So how to select a particular point in
the complex to
Dear All,
I have copied and patched the plumed script plumed_gromacs-4.5.5.sh,
given in the patches directory. But after doing that, while running
some umbrella sampling it's not printing the COLVAR file, only the
simple md is running there.
So, can anyone help me in this regard?
Thanks
--
Hi,
I was also facing the same problem. If you check your pressure during
this NPT run, u can see that it got increased to a higher value. I had
posted the same problem few days back, u can follow the thread. It
seems MTTK is not stable enough and is not performing well in this
context. So I have
vmd protein.trr protein.gro
then go to the representation and then write 'all not water' with
cartoon representation, u will get the protein only.
Cheers,
Tarak
On Thu, Nov 22, 2012 at 12:58 PM, rama david ramadavidgr...@gmail.com wrote:
Dear,
-o MT.PnoH.xtc instad of xtc extenstion use
-users-
boun...@gromacs.org] Im Auftrag von tarak karmakar
Gesendet: Mittwoch, 21. November 2012 15:03
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] pressure_coupling
Thanks for the information Flo.
Before doing NPT I have already equilibrated my system by heating it from
0K
2012 18:33
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] pressure_coupling
On 11/20/12 12:29 PM, tarak karmakar wrote:
Thanks Justin for the quick reply.
Is there any problem with the algorithms ??
I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE
parameters ?
On Tue, Nov 20, 2012 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/20/12 11:26 AM, tarak karmakar wrote:
Dear All,
I want to keep the pressure at 1.0 bar during the NPT simulation. But
it is fluctuating around 130 bar. So can anyone please inform me
whether I have
thanks a lot Justin
I'll try to follow this protocol.
On Sun, Nov 11, 2012 at 8:59 AM, Justin Lemkul jalem...@vt.edu wrote:
On 11/10/12 10:27 PM, tarak karmakar wrote:
Thanks Justin
If I want to constrain all the bonds in the substrate molecule present
inside the enzyme cavity then along
Thanks Justin
If I want to constrain all the bonds in the substrate molecule present
inside the enzyme cavity then along with SHAKE what I need to use ?
On Fri, Nov 9, 2012 at 5:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/8/12 11:36 PM, tarak karmakar wrote:
Thanks Justin
As you
:
Double entries in block structure. Item 5247 is in blocks 1371 and 1370
Cannot make an unambiguous inverse block.
Please suggest me the exact protocol.
Thanks
On Fri, Nov 9, 2012 at 2:18 AM, Justin Lemkul jalem...@vt.edu wrote:
On 11/8/12 1:07 PM, tarak karmakar wrote:
Dear All,
In my
Dear All,
As I am facing the following problem while using SHAKE to constrain
some bonds, I have checked the mailing list but I think, this issue
has not been resolved. So if anyone knows the solution kindly inform
me.
Program mdrun, VERSION 4.5.5
Source code file: invblock.c, line: 79
Fatal
confused how to implement constraints algorithm for these
type of problem.
Thanks
On Wed, Nov 7, 2012 at 11:54 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/7/12 10:46 AM, tarak karmakar wrote:
Dear All,
As I am facing the following problem while using SHAKE to constrain
some bonds, I have
PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/12/12 10:39 AM, Dr. Vitaly Chaban wrote:
On 10/12/12 2:42 AM, tarak karmakar wrote:
Dear ALL,
In my protein I need to constraint the length between the Metal and
the N of Histidine residues. In the .rtp file I didn't specify this
Mn-N
...@vt.edu wrote:
On 10/3/12 6:00 AM, tarak karmakar wrote:
Dear All,
Is it possible to deal a protein with tyrosyl radical in Molecular
Dynamics Simulation ?? If possible can you please provide me the
reference or literature where I can find the force field parameters
for tyrosyl radical
jalem...@vt.edu wrote:
On 10/3/12 7:49 AM, tarak karmakar wrote:
Thanks Justin,
Actually if I would remove the proton from the tyrosine -OH and add
the corresponding charge of the Hydrogen to the phenolic oxygen to
keep the residue neutral then wouldn't it be convenient to think as if
it's
) and atom no. 879 (ligand atom) with respect to time)
On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 20/09/2012 2:05 PM, tarak karmakar wrote:
Thanks Justin.
But in my case I want to plot the distance between one atom in the
backbone of the protein
thanks a lot Mark
On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 20/09/2012 4:21 PM, tarak karmakar wrote:
Thanks Mark.
I was using the following command as I got it in the manual.
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg
But I could
Thanks Mark ,
I got it now :)
On Thu, Sep 20, 2012 at 3:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 20/09/2012 7:31 PM, tarak karmakar wrote:
Dear All,
I need to plot a specific dihedral in my protein and I have to
see how it is changing with time. So while doing
Dear All,
I want to calculate the distance between the nitrogen atom present in
the ligand and the H- attached to the backbone of the protein along a
long trajectory. So can anyone suggest me how to consider these two
atoms to calculate and plot the distance along with the time ?
--
Tarak
--
wrote:
On 9/19/12 2:55 PM, tarak karmakar wrote:
Dear All,
I want to calculate the distance between the nitrogen atom present in
the ligand and the H- attached to the backbone of the protein along a
long trajectory. So can anyone suggest me how to consider these two
atoms to calculate
...@anu.edu.au wrote:
On 17/09/2012 10:01 PM, tarak karmakar wrote:
Dear All,
I want to have one of tyrosine residues in my protein to
be unprotonated. I am using amber force field for the simulation. But
in aminoacid.rtp there is no entry for the unprotonated one. So I am
adding
Dear All,
I want to have one of tyrosine residues in my protein to
be unprotonated. I am using amber force field for the simulation. But
in aminoacid.rtp there is no entry for the unprotonated one. So I am
adding it by myself in to the .rtp file. Now I am bit confused with
the charge
Dear All,
In my protein pdb file I am changing the protonation state of residue
and giving some other name to it . Now after creating the .gro file I
see that the residue present before the modified one has been
considered as the C-terminal and it is adding one extra oxygen atom to
it. I am
Thanks a lot Justin.
On Wed, Aug 29, 2012 at 11:57 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/29/12 2:19 PM, tarak karmakar wrote:
Dear All,
In my protein pdb file I am changing the protonation state of residue
and giving some other name to it . Now after creating the .gro file I
Dear All,
I am using AMBER94 force-field for my protein. In the original force
field paper the dihedral functional form has been given as (V/2)[ 1 +
cos(nPhi - gamma)] but in GROMACS(4.5.4) manual I see the (1/2)
factor is not there [ eq 4.62]. So is this internally handled in
GROMACS or should
Dear All,
In my simulation I want the temperature of the system to be reached at
300 K only after 3 ps. But after 3ps I see temperature became 402 K.
So am I doing any mistake in the '.mdp' file given below?
define= -DFLEXIBLE
constraints= h-bonds
integrator = sd
Thanks a lot for the quick reply...probably I have
overlooked this point earlier
..now I'm getting it properly
On Thu, Aug 16, 2012 at 10:33 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/16/12 12:57 PM, tarak karmakar wrote:
Dear All,
In my simulation I
then why should I multiply by the
factor 180/pi ? Can you please make it clear, I gotta confused.
Thanks,
Tarak
On Tue, Aug 14, 2012 at 7:17 PM, David van der Spoel
sp...@xray.bmc.uu.se wrote:
On 2012-08-14 14:27, tarak karmakar wrote:
Dear All,
In the manual I see the unit of the k{theta
Hi Mark,
I have used the following .mdp file for the run and got the excess
temperature for the system; it has reached the desired temp at around
150-155 ps. But I need to reach the temp at after 300 ps.
Thanks,
define = -DFLEXIBLE
constraints= h-bonds
integrator
Dear All,
Is there any way to add a specific number of water ( let say 650
water) molecules while dissolving the solute in a given box ?
Thanks,
Tarak
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
*
)Segments: 1
Info)Fragments: 669 Protein: 1 Nucleic: 0
On Tue, Aug 14, 2012 at 9:46 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/08/2012 2:02 PM, tarak karmakar wrote:
Dear All,
Is there any way to add a specific number of water ( let say 650
water) molecules while dissolving
in the system before adding another 612?
I don't know how VMD counts waters, but another way is to grep -c for SOL in
the resulting gro file and divide by 3.
On 2012-08-14 10:07:54AM +0530, tarak karmakar wrote:
Thanks for the quick reply, I have given this command to add 612 water
molecules
Oh !!
I got it it is not the -nmol but '-maxmol'
thanks to both of u...:)
On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai p...@uab.edu wrote:
hmm. What happens if you try -maxsol instead of -nmol?
On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote:
This is the ala.gro (alanine
sorry '-maxsol'
On Tue, Aug 14, 2012 at 11:24 AM, tarak karmakar tarak20...@gmail.com wrote:
Oh !!
I got it it is not the -nmol but '-maxmol'
thanks to both of u...:)
On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai p...@uab.edu wrote:
hmm. What happens if you try -maxsol instead
Dear All,
I did the simmulated annealing for a protein where I wanted to
increase the temperature from 0 K to 300 K after 300 ps. But after the
simulation run I see the temp got increased up to 400 K and so.
So can anyone tell me whether I am doing any mistake ?
The .mdp file for the run is as
Dear All,
I am studying a molecule which is changing its conformation
during a reaction. So I want to calculate free energy for the
conformational change. I am planning to do Umbrella sampling for this
purpose. But what is the way to handle the dihedral angle as a
Collective Variable
Dear All,
I am studying a molecule which is changing its conformation
during a reaction. So I want to calculate free energy for the
conformational change. I am planning to do Umbrella sampling for this
purpose. But what is the way to handle the dihedral angle as a
Collective Variable
value. Is that
because my system is not minimized / equilibrated properly ?
Any suggestion ?
Thanks
On Mon, Jul 30, 2012 at 7:33 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 30/07/2012 3:39 AM, tarak karmakar wrote:
Dear All,
In my initial protein pdb structure I have added some
Dear All,
In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run, I plotted the RMSD of the resulting
see its not a big issue. Look at the atom types of the particular
RESIDUE in the pdb file and also have a look into the atom types
present in the rtp file. Now if these are matching properly then you
can choose any convenient name for that particular residue in the rtp
file. But the name of the
Dear All,
The protein with which I'm working with, contains Zn metal and it
has tetrahedral coordination site. There are HISTIDINE side chains
within distance ~ 2.3 to 2.4 . So my questions are as follows
(1) In that distance range there is no possibility to form a covalent
bond between Zn
Dear All ,
I wanted to keep all the molecules other than water fixed [
positiion restraints]. So for that I have performed short NVT
[simulation with DEPOSRE] after minimization, but while seeing the
movie of the trajectory in VMD I see the protein backbone is moving.
So did I miss
Dear All,
While running minimization I imposed the the condition for the
minimization as to be converged only at Fmax 10 . But I got the
following
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax 10
Double precision normally
many times but didn't get
proper clue; in one of those mails I saw someone has dealt with some
dummy atoms. I could not able to digest that logic.
On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 24/07/2012 3:21 PM, tarak karmakar wrote:
Dear All,
I am
, tarak karmakar wrote:
Dear All,
I am constraining one angle in my protein sample by incorporating [
constraints ] block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the following error
clue; in one of those mails I saw someone has dealt with some
dummy atoms. I could not able to digest that logic.
On Tue, Jul 24, 2012 at 11:01 AM, Mark
Abrahammark.abra...@anu.edu.au
wrote:
On 24/07/2012 3:21 PM, tarak karmakar wrote:
Dear All,
I am constraining one angle in my
[ system ]
; Name
Protein in water
[ molecules ]
; Compound#mols
Other_chain_A 1
SOL 622
--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
JNCASR
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
Thanks for the reply.
But then what should I give as Kb [ bond stretching constant ] in the
ffbonded.itp file ? should I give 00.000 there or something else ???
On Mon, Jul 23, 2012 at 4:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/23/12 2:39 AM, tarak karmakar wrote:
Dear All
, tarak karmakar wrote:
Thanks for the reply.
But then what should I give as Kb [ bond stretching constant ] in the
ffbonded.itp file ? should I give 00.000 there or something else ???
Constraints make bonds rigid. The force constant is irrelevant.
-Justin
On Mon, Jul 23, 2012 at 4:11 PM
that
a bond can rotate before LINCS will complain
--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
JNCASR
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please
Dear All,
I am constraining one angle in my protein sample by incorporating [
constraints ] block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the following error
Program grompp, VERSION 4.5.5
to the simulation.
Thanks in advance,
Tarak
--
Tarak Karmakar
Molecular Simulation Lab.
C.P.M.U
JNCASR
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http
at that particular pH ? [
Protein Calculator !! ]
Thanks in advance.
--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809
--
gmx-users mailing
Dear All,
Please suggest me any paper/article that contains force field
parameters for Mn 2+ .
Thanks
--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
/doi/10.1002/anie.201202032/abstract
hope it helps
On 07/09/2012 12:21 PM, tarak karmakar wrote:
Dear All,
Please suggest me any paper/article that contains force field
parameters for Mn 2+ .
Thanks
--
-
Andrea Spitaleri
sorry it's my mistake .
thanks a lot for the reply.
On Mon, Jul 9, 2012 at 10:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/9/12 1:21 PM, tarak karmakar wrote:
Oh !! nice work
Thanks a lot for the quick reply. But I'm very sorry to inform you
that whichever table
) aminoacids.rtp
3) ffnonbonded.itp
4) ffbonded.itp
5) spc.itp
6) ions.itp
now while giving the command
pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top
how can I make use of all these force field files present in my current
working directory ?
Thanks in advance.
--
*Tarak Karmakar
Molecular
:
On 15/06/2012 4:27 PM, tarak karmakar wrote:
Dear All,
In my protein pdb file I have changed some of the amino acid residue
names. So accordingly I have changed corresponding residue names in force
filed files and kept all the files [ modified and unmodified ] in my
current working
Thanks a lotnow it's working:)
On Fri, Jun 15, 2012 at 2:00 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 15/06/2012 6:21 PM, tarak karmakar wrote:
Hi,
Thanks for the reply.
One thing, while giving the '-ff' flag it is asking for some string. So I
renamed all my force
be highly appreciated.*
* Thanks
Tarak
--
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *
--
gmx-users mailing listgmx
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka
1 - 100 of 102 matches
Mail list logo
