On 11/3/17 4:49 AM, Adriano Santana Sanchez wrote:
Dear all,
I am a beginner with gromacs and I have already done some online tutorials.
I am now trying to create from a PDB coordinate file (a CTAB molecule) the
corresponding .GRO and .TOP files to run MD simulations.
gmx pdb2gmx
On 11/3/17 8:17 AM, Hermann, Johannes wrote:
Dear Justin,
thanks for the hint with the CHARMM-formatted topology and parameter
files! That is great help! I had a different atom number compared to
NAI and NADH because I had a different (non-physical) protonation
state. The text drawing
It seems that ctab.pdb contains residue 'XXX'. Verify that with pdb viewer such
as pymol etc.
Residue 'XXX' is not standard amino acid with 3 letter code so in lead to such
error.Maybe you can delete it with same pdb viewer, or fix that naming error
somehow. Its up to you to decide.
On
Dear Justin,
thanks for the hint with the CHARMM-formatted topology and parameter
files! That is great help! I had a different atom number compared to NAI
and NADH because I had a different (non-physical) protonation state. The
text drawing helped me a lot to figure out the few Nomenclature
Hello
I'm trying to obtain the PMF of an umbrella simulation using WHAM, but i get
this error which i have no ideea how to solve :
Command line:
gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
Note: Will use 8 OpenMP threads.
Found 15 tpr and 15 pull force files in
On Fri, Nov 3, 2017 at 2:00 AM, minky son wrote:
> Dear gmx user,
> I’m studying about alchemical free energy calculation.
> I have been read some articles about restraints during free energy
> calculation, they referred the procedure in the article (
>
On 11/3/17 9:36 AM, Wes Barnett wrote:
On Fri, Nov 3, 2017 at 2:00 AM, minky son wrote:
Dear gmx user,
I’m studying about alchemical free energy calculation.
I have been read some articles about restraints during free energy
calculation, they referred the procedure in
Hey Justin,
thanks - again - for your reply!
Now I get duplicated parameters warnings and errors:
WARNING 1 [file fmn.prm, line 5]:
Overriding Bond parameters.
old: 0.1295 405848 0.1295
405848
new: CG2R64 NG2D1 1 0.1414
Force field in gromacs reads only standard amino acids/DNA/RNA residue. In
your pdb file residue name XXX is not defined in gromos ff. If your system
is other than protein then use ATB to generate topolgy.
One thing to try is to build the CTAB molecule with gmx x2top. You'll need to
be careful about what it produces, but it can be helpful.
===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular
Dear all,
I am a beginner with gromacs and I have already done some online tutorials.
I am now trying to create from a PDB coordinate file (a CTAB molecule) the
corresponding .GRO and .TOP files to run MD simulations.
gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce
then choose
Hi,
I've been trying to study a protein-ligand PMF using umbrella sampling
strategy.
So far, I have obtained the PMF following the tutorial and after performing
bootstrapping the error is estimated to be at most 0.4 kcal/mol.
Now, given the error value can I comment about changes like 2-3
Dear gmx user,
I’m studying about alchemical free energy calculation.
I have been read some articles about restraints during free energy calculation,
they referred the procedure in the article
(http://pubs.acs.org/doi/pdf/10.1021/jp0217839).
I tried to search mailing list, but still I couldn’t
Hi all,
It appears that the external field is refusing to move the ions when
walls are present. I am comparing two setups of a system that has an
aqueous bath (1M KCl) split by a semi-porous (infinitely selective for
cations) membrane in XY. The only difference between them is that one is
The nucleic acid builder should do what you want:
http://structure.usc.edu/make-na/
Cheers
Tom
On 03/11/17 19:54, Dan Gil wrote:
Hi,
I would like to use the parmbsc1 force field to simulate DNA. I installed
the force-field and am now actually running a simulation with a Drew
Dickerson
Hi,
I would like to use the parmbsc1 force field to simulate DNA. I installed
the force-field and am now actually running a simulation with a Drew
Dickerson Dodecamer structure I downloaded from the RCSB database.
Now I would like to generate my own structures and simulate them. I tried
using
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