Dear gmx users,
I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names
were modified according to the rtp file of the force field. Yet, I get the
following error while I perform pdb2gmx command:
Fatal error:
Residue 4 named GLC of a molecule in the input file was
Dear gmx users
I am trying to simulate my complex using amber99sb ff. There is no amber
tutorial in gromacs. I need to know how dispersion correction set in the
.mdp files . I can not understand the definitions of DispCorr in mdp
option. Should I put it on EnerPres or no ?
Would you please
Dear, I want to combine proteins to merge into single pdb but I get this
error below.
Command line:
gmx trjcat -f 10ns.pdb 15ns.pdb 40ns.pdb 60ns.pdb 90ns.pdb -o all.pdb
Reading frame 0 time 1.000'', 3420 atoms
Last frame 0 time 1.000
Reading frame 0 time
>1. I wonder how I can prove that the core part looks like a sphere? or how
>can I measure the Sphericity of the core part? Does Gromacs offer a tool
>for that?
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-gyrate.html
Then compare rx, ry, rz and/or eccentricity
Catch ya,
Dr.
Paper explaining dispersion correct, and what it is:
http://dx.doi.org/10.1021/jp0735987
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
Thank you for reply
[ Input values in mdp file ]
nstlist = 10
nsttcouple = -1
After gmx mdrun, ‘nstlist’ is automatically changed from 10 to 50.
I expected that both ‘nstlist’ and ‘nsttcouple’ would be changed to 50,
because ‘nsttcouple=-1’ means ‘nsttcouple=nstlist’.
But, nstlist =50 and
Hello,
You can also do it with parmed from Amber, here are the python commands:
import parmed as pmd
#convert prmtop and inpcrd into top and gro
amber = pmd.load_file('1N55_apo.prmtop','1N55_apo.inpcrd')
#
amber.save('topol.top')
amber.save('ions.gro')
#
On 11/7/18 10:07 AM, Rahma Dahmani
Dear colleagues,
we would like to invite you to the 4th Drug Design workshop which
will be held on 21-25 January 2019 in Olomouc (Czech Republic). It is
focused on practical applications of different chemoinformatic tools and
approaches for drug development. This might be interesting for
Use acpype
On Wed, Nov 7, 2018, 2:38 PM Rahma Dahmani wrote:
> Hi Gromacs Users,
> I need to convert AMBER topology and coodinates files to GROMACS top and
> gro files , How can-I do that ?
> PS: I already tested a script on line (amb2gmx) but it didn't work ...
>
Hi Gromacs users,
I used antechamber tools to genrate a topology and coordinates files for my
ligand, then i used acpype to convert them to gromacs files (.top and
.gro), then *i added manually water FF in topology file* since i want to
run MD simulation of ligand in water
I double checked
On 11/5/18 12:16 PM, Karpurmanjari Kakati wrote:
Dear Justin,
I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the
aminoacids.rtp file . I have all the files of OPLS AA force field in my
working directory.
For that I tried to generate the initial rtp format file from the
On 11/5/18 1:19 PM, ABEL Stephane wrote:
Hello again,
Does the GROMACS team have some suggestions to help me to resolve my problem
with the output of gmx densmap and xpm2ps to an eps/pdf with all the ticks in
the x/y axis (see below)? Since it seems a small bug should I fiil a redmine?
Dear gmx users,
In gromacs manual,
“nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
unless nstlist <=0, then a value of 10 is used.”
When I did grompp with the following mdp options,
nstlist = 20
tcoupl = berendsen
nsttcouple = -1
tau-t = 0.1
I got a warning
On 11/3/18 2:15 PM, rose rahmani wrote:
On Sat, 3 Nov 2018, 19:56 Justin Lemkul
On 11/2/18 11:36 AM, rose rahmani wrote:
but this is output of -oall. its not a single value?!
You are asking in your command for all interatomic distances between the
groups (presumably, because you haven't
nsttcouple=10 means that nsstcouple*dt(2fs, I guess)=0.02 and your
tau-t=0.1 (5 fold)
when nsttcouple=20, nsstcouple*dt=0.04 so your tau-t is only 2.5 fold. I
think so
On Wed, Nov 7, 2018 at 3:43 PM minky son wrote:
> Dear gmx users,
>
>
> In gromacs manual,
>
> “nsttcouple: The default value
On 11/7/18 9:48 AM, Rahma Dahmani wrote:
Hi Gromacs users,
I used antechamber tools to genrate a topology and coordinates files for my
ligand, then i used acpype to convert them to gromacs files (.top and
.gro), then *i added manually water FF in topology file* since i want to
run MD
On 11/7/18 9:43 AM, minky son wrote:
Dear gmx users,
In gromacs manual,
“nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
unless nstlist <=0, then a value of 10 is used.”
When I did grompp with the following mdp options,
nstlist = 20
tcoupl = berendsen
nsttcouple
On 11/5/18 5:07 AM, CROUZY Serge 119222 wrote:
Hello Justin-
In MY pullx first column is Time and second column is absolute coordinate of
the COM of the pulled group
Maybe we are missing an option which would print X and dX in the pullx files - one of the
pull-print stuffs ???!!.. In that
Hello Justin,
It is not clear to me it is bug. but I "think" that in these particular case
densmap does not truncate/rounds the data according to the bin value (i.e.
0.05) I used in gmx densmap command line. To correct this I wrote a short
script that change the x-y values like where the x/y
Dear all,
I have two types of molecules (molecule number from each 56 and 29
respectively) in water, the MD simulation gives me a core-shell like system
in which the core part contain one of the molecule type and the shell is
the another one that accumulate around the surface of the core.
Dear all,
I have two types of molecules (molecule number from each 56 and 29
respectively) in water, the MD simulation gives me a core-shell like system
in which the core part contain one of the molecule type and the shell is
the another one that accumulate around the surface of the core.
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