Hello, any one plz help
Version: 5.0.7
FF: 43a1
Heme topology is present in almost all the force fields. I want to simulate
corn (Pdb id :IHHO) containing heme. When I run simulation I get this error :
"Residue HEM not found in residue topology database". As heme topolo
Hello, Hopefully, You are all doing well. Version: 5.0.7 FF:
43a1 Spc watermodel
Heme topology is present in almost all the force fields. I want to simulate
corn (Pdb id :2R50) containing heme. When I run simulation I get this error :
"Residue HEM not found in residue topolo
On 08/02/17 23:48, Victor Rosas Garcia wrote:
Hello everybody,
I am having problems with gmx solvate. I am trying to solvate a small
peptide with a solvent shell 1.2 nm thick. When I use the following
command line:
gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p
../to
Hi!
I’ve been trying to apply a distance restraint on a metal and 4 other
coordinating atoms.
So I made 5 indices (each for one of the ligating atom and the metal) and then
made 4 distance restraint .itp files with gmx genrestr.
gmx genrestr -f gro -n mdx -o itp -disre -disre_dist 0.1
So the pai
5 ns is not long enough to equilibrate the APL, and it's a time-averaged
property in experiment, so looking at one frame is not as good as averaging
over tens of ns of simulation. Try running for 100 ns and taking the average of
the last 50 ns. Also, what APL do you get and what value do you con
Dear Gromacs users,
As part of my M.Sc. thesis I should do MD simulation. For this purpose,
at first I intended to regenerate a rational Area per lipid with good
agreement with experiment as verification of my subsequent MD
simulations. I downloaded the initial .pdb file from Dr. tieleman lab
web
Hello everybody,
I am having problems with gmx solvate. I am trying to solvate a small
peptide with a solvent shell 1.2 nm thick. When I use the following
command line:
gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p
../topol.top
I get the following message:
Yes, That was really a good news. Thanks AMBER.
As you suggest I try to find the free energy for these two situations. I
hope can find any result.
Mohamad
On Wed, Feb 8, 2017 at 11:48 PM, Mark Abraham
wrote:
> Hi,
>
> Well that's relatively good news :-) You can likely use the same kinds of
> f
On 2/8/17 12:48 AM, Subashini .K wrote:
Hi,
Thank you for the reply.
I got RDF for distances up to 1.772 angstrom (in x-axis) using the code
mentioned.
GROMACS does not output anything in Angstrom, so be sure you understand the
units you're seeing. Also the "code" you showed before i
Hi,
Well that's relatively good news :-) You can likely use the same kinds of
free-energy methods that are used e.g. for relative free-energy of binding
of one drug molecule over another to a protein... your "drug" is just the
ion, of course. See various tutorials. First challenge is to understand
Dear Mark,
Thanks for your reply,
Recently I came across the following tool that is developed by AMBER and it
seems it can define a FF to model for As. It actually covers 80 different
metals:
http://ambermd.org/tutorials/advanced/tutorial20/bonded_model.htm
http://pubs.acs.org/doi/abs/10.1021/acs.
Hi,
I would also strongly recommend replicating some existing work on heme with
Fe2+, before grappling with unknowns.
Mark
On Wed, Feb 8, 2017 at 3:25 PM Justin Lemkul wrote:
>
>
> On 2/8/17 1:47 AM, Mehreen Jan wrote:
> > Hello, anyone plz help Hopefully you all are doing well. I am using FF:
On 2/8/17 1:47 AM, Mehreen Jan wrote:
Hello, anyone plz help Hopefully you all are doing well. I am using FF: 43a1
Spc watermodel version 5.0.7.
I know parameters for Heme are already available and that is for FE2+. I want
to perform MD simulation for FE3+. While running simulation I get error
Hi,
On Wed, Feb 8, 2017 at 2:29 AM wrote:
> Hi people,
> I have computer with 2x Xeon E5-2660 with Radeon Fury (as someone here
> recomended it as quite decent card (not the best one ;-) of course ).
> System is debian (testing). I have previously R9 280X instead and it worked
> without problem.
Hi,
First, you need to find a force field that can model As, and then show it
has some usefulness for relative binding affinity. But it seems wildly
unlikely that any will exist that are useful. Classical force field models
are very unlikely to be able to do a good job of this.
Mark
On Wed, Feb
Thank you for reply
I am using Justin's perl script for calculating hydrogen bond existence. I
am following the same procedure like deleting all the above lines before
[hbond_protein_drug] and using pdb file with no chain ID etc. I have read
the out file of hbm and hbn also. Then what could be the
Dera Tasneem,
First thing to check is if you have read the -hbn or -hbm output upside down.
This is a common mistake. Seriously.
Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...
Dear all
I am calculating hydrogen bond between protein and drug molecule using gmx
hbond tool. I am using default value for hydrogen bond radius.
Here is the command:
gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm
hbond.ndx
I am selecting group 1 and 13.
It shows many hydro
Dear Maria,
I’m not saying that it never makes a difference for the topology generation,
but it depends on the quality of your input structure. Justin and I both gave
examples of why you might want to use it. When you do, -ignh ignores the
hydrogens in the input pdb and uses the rtp to model ne
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