Hi all,
I have modelled a structure and I want to minimize it using GROMACS
but while generating the topology file using pdb2gmx command I am
getting the following error :-
Atom HN1 in residue LEU 1 not found in rtp entry with 9 atoms
while sorting atoms. Maybe different protonation
Hello!
Since you have modelled the structure, so the important thing is the
position of the heavy atoms and not of the hydrogens, you can just do what
GROMACS asks you to do:
pdb2gmx . (all the things that you have to put) .. -ignh
This flag will make pdb2gmx ignore the hydrogens and rep
Thanks for the help mdrun step is going on now .. but I wanna ask one
thing that how can I visualize the minimized structure .. The
structure which I used initially is the minimized structure or not ??
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puduc
Hi all
What is the best interval for saving configurations in full md step? (every
what ps?)
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Hi all,
I want to calculate the non-bonded interactions (LJ+Coulomb) between two
sub-groups when they are within the cutoff distance. The sub-groups are
only parts of the whole energy groups used in my .mdp file. Given the
partial charges of the atoms involved are easy to get from the
"top.atoms.
Hi,
it depends. Firstly how strong are the configurations related over time.
Then the maximum of your harddisk. Generally it is in the order of
magnitude of ps.
shahab shariati wrote:
> Hi all
>
>
>
> What is the best interval for saving configurations in full md step? (every
> what ps?)
>
>
It also strongly depends on what analysis you try to do. For
autocorrelation you should sample frequently enough, for other
configurational analysis, you don't need so many points, for
covariance analysis you should aim for a number of frames three times
the number of atoms you want to analyze.
Ch
On 08/02/10 21:03, Baofu Qiao wrote:
Hi all,
I want to calculate the non-bonded interactions (LJ+Coulomb) between two
sub-groups when they are within the cutoff distance. The sub-groups are
only parts of the whole energy groups used in my .mdp file. Given the
partial charges of the atoms involve
On 08/02/10 19:40, bharat gupta wrote:
Thanks for the help mdrun step is going on now .. but I wanna ask one
thing that how can I visualize the minimized structure ..
Search the GROMACS webpage for visualisation software suggestions.
The
structure which I used initially is the minimized struc
Chandan Choudhury wrote:
Hello gmxusers !!
gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from
#spc_25_eq.trr.1#. mdrun was stopped due to insufficient space)
Checking file #spc_25_eq.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 2000.000
#
Hi all,
I had followed all the 7 steps of gromacs beginners tutorial and I
have a doubt that during the minimization step .. which structure is
minimized one ?? The one that i used for the minimization step ...
Pls reply
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pond
bharat gupta wrote:
Hi all,
I had followed all the 7 steps of gromacs beginners tutorial and I
have a doubt that during the minimization step .. which structure is
minimized one ?? The one that i used for the minimization step ...
A structure is only minimized if you ran EM, or the program
Hi Mark,
Thanks for your reply!
I want to use the pre-saved trajectory. Based on the distance criteria,
calculate the Coulomb and LJ interaction. However, I don't know the data
structure related with the LJ parameters. Do you have related knowledge?
The mdrun -rerun might be impossible for me,
Nice! Thank you!
> Muhammad Naqvi wrote:
> > Hi all,
> > Wonderful community here! FAQs andManuals on one side, nothing beats
> the advice of experts. Whoever started this forum, thank you. I am
> learning a lot.
> >
> > I have a question of my own. I am trying to see the interaction of
> cert
On 08/02/10 23:07, Baofu Qiao wrote:
Hi Mark,
Thanks for your reply!
I want to use the pre-saved trajectory. Based on the distance criteria,
calculate the Coulomb and LJ interaction. However, I don't know the data
structure related with the LJ parameters. Do you have related knowledge?
The p
Dear All,
I am having problems compiling gromacs 4.0.7 in parallel. I am following the
Quick and Dirty Installation instructions on the gromacs webpage.
I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7
following these instructions.
Everything seems to compile OK and I get all
Jennifer Williams wrote:
Dear All,
I am having problems compiling gromacs 4.0.7 in parallel. I am following
the
Quick and Dirty Installation instructions on the gromacs webpage.
I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7
following these instructions.
Everything seem
Dear Justin
Thanks for your reply.
I didnot get any fatal error. Since, the mdrun has started (mdrun -s
spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e
spc_25_eq.edr -g spc_25_eq.log -append yes ), it has created new state.cpi.
So I now I cannot verify it. From now, I will defin
Chandan Choudhury wrote:
Dear Justin
Thanks for your reply.
I didnot get any fatal error. Since, the mdrun has started (mdrun -s
spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e
spc_25_eq.edr -g spc_25_eq.log -append yes ), it has created new
state.cpi. So I now I cannot
Hi Tom!!
Thanks for the information. I went through the paper and added the new O3
atom type. One unusual thing I noticed was that the sum of the partial
charges on the atoms of AT P at the last column of
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prepfile
is -12
As Justin said give the command line options for mdrun and also check that
your mpi environment is running. Better to run a parallel job and check its
output.
Chadnan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul wrote:
>
>
> Jennifer Williams wr
Are you sure you added it up correctly? I get a number very close to -4.
There is no hydrogen on the gamma phosphate as it was parameterised in
this way. If the environment in which your ATP is located suggests that
the gamma phosphate should be protonated then you need to use other ATP
parame
Thanks Tom.
Some how only the negative charges were being added in spreadsheet. So, I
got charge around -12.
I am simulating 1QHH. It has ATP in it, the structure of the ligand in the
rcsb (http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH) shows ATP
with hydrogen.
--
Chandan kumar Chou
I had a simple query regarding the rtp file . What does the '+' and '-' sign
indicates in the following dihedral inforamtion:
[ dihedrals ]
CA C+N+Hbackbone_prop_1
O C+N+Hbackbone_prop_2
-C NCACBbackbone_prop_3
-C NCA C
Chandan Choudhury wrote:
I had a simple query regarding the rtp file . What does the '+' and '-'
sign indicates in the following dihedral inforamtion:
[ dihedrals ]
CA C+N+Hbackbone_prop_1
O C+N+Hbackbone_prop_2
-C NCACBbackbone_pr
Well it is up to you to decide (or find out) if you think it should be
protonated or not. I just had a quick look in the PDB file and there are
no hydrogens on the ATP, plus the crystal structure was determined using
an ATP analogue so I would not solely base my judgement on a structure
of the
Ok, here's what i've got:
Gromacs version 4.0.5.
Both platforms are Linux, icc 10, fftw 3
compile option: ./configure --enable-mpi
thanks for your help!
Gard
Gard Nelson wrote:
> Hi all,
> I'm trying to simulate a solvated membrane using Berger's lipids. When
> I run grompp, i get the followi
Users,
Thanks for the response. To further clarify I am running rhel5 on a
single quad machine. I tried Chandan Choudhury's suggestion and that
hello world program doesnt output anything on my machine. Here is what
i did:
1. mpicc mpitest.c -o test
2. mpirun -np 2 test
I made a slight cha
On Mon, 2010-02-08 at 13:48 -0500, Matthew L. Danielson wrote:
> Users,
>
> Thanks for the response. To further clarify I am running rhel5 on a
> single quad machine. I tried Chandan Choudhury's suggestion and that
> hello world program doesnt output anything on my machine. Here is what
> i
Dear gromacs users:
I am trying to get the topology file for oxy-hemoglobin. As
suggested below in the link below, I am trying to modify my itp or rtp
file.
http://osdir.com/ml/science.biology.gromacs.user/2006-07/msg00236.html
But, if anybody has already constructed rtp file for oxy hem
Quoting Gard Nelson :
> Ok, here's what i've got:
>
> Gromacs version 4.0.5.
> Both platforms are Linux, icc 10, fftw 3
> compile option: ./configure --enable-mpi
>
The vast majority of Gromacs programs (read: anything not called "mdrun") are
not MPI-enabled. Users have reported weird activity
Hello All,
I've taken the average peptide structure from two different MD simulations
using g_rmsf. Is there a method for calculating the RMSD between those two
structures? The only difference between the two peptides is a single residue
mutation. Thanks.
--Venk
Justin,
This is in response to your mail on this subject. My objective was to do
an NPT simulation of a 200 particle fluid using Lennard-Jones parameters
only. I also used the atomic number, atomic mass, and Lennard-Jones
parameters(sigma in nm and epsilin in KJ/mol) for the oxygen atom, and the
Lum Nforbi wrote:
Justin,
This is in response to your mail on this subject. My objective was to
do an NPT simulation of a 200 particle fluid using Lennard-Jones
parameters only. I also used the atomic number, atomic mass, and
Lennard-Jones parameters(sigma in nm and epsilin in KJ/mol) for
On 09/02/10 10:20, V Hariharan wrote:
Hello All,
I've taken the average peptide structure from two different MD
simulations using g_rmsf. Is there a method for calculating the RMSD
between those two structures? The only difference between the two
peptides is a single residue mutation. Thanks.
On 09/02/10 09:04, Justin A. Lemkul wrote:
Quoting Gard Nelson:
Ok, here's what i've got:
Gromacs version 4.0.5.
Both platforms are Linux, icc 10, fftw 3
compile option: ./configure --enable-mpi
The vast majority of Gromacs programs (read: anything not called "mdrun") are
not MPI-enabled.
Hi,
I'm facing a problem with GROMACS that appears pretty simple, actually. I'm
trying to set a dodecahedron box but all I can get is a triclinic box. For
that, I'm using the following line:
*
editconf -f pMHC -bt dodecahedron -o -d 1 *
Am I doing something wrong?? Another problem, different fro
Maurício Menegatti Rigo wrote:
Hi,
I'm facing a problem with GROMACS that appears pretty simple, actually.
I'm trying to set a dodecahedron box but all I can get is a triclinic
box. For that, I'm using the following line:
/
editconf -f pMHC -bt dodecahedron -o -d 1 /
Am I doing something
On 09/02/10 12:12, Maurício Menegatti Rigo wrote:
Hi,
I'm facing a problem with GROMACS that appears pretty simple, actually.
I'm trying to set a dodecahedron box but all I can get is a triclinic
box. For that, I'm using the following line:
/
editconf -f pMHC -bt dodecahedron -o -d 1 /
Since a
Hi,
> You can post-process your trajectory using "trjconv -pbc mol -ur compact" to
>see the real
> representation.
The real representation is the infinite periodic system; there is no
box shape there. For representation of a single unit cell you can take
any cut that is consistent with the latti
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