hello,
i want to calculate the contact map between two different proteins. Using
mdmat it is possible to calculate the contact map within a protein. But can
anyone please suggest me how i can calculate the inter-residue contact map
between two proteins using gromacs.
thanking you
shahee
--
Hi Micholas,
Thank you for your input, I was hoping to avoid that... But I guess I have to
do it this way.
Best,
Ben
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Smith,
Micholas D.
Sent: 12 August 2019 13:13
To:
On 8/14/19 7:29 AM, DEEPANSHU SINGLA wrote:
I used the CGenFF program for generating the ligand topology. The GROMACS
tutorial recommends the manual reparameterization of force field in case
the penalty score exceeds 50. My ligand penalty scores exceed 50 and don't
know how to change the
On 8/14/19 8:52 AM, afsaneh maleki wrote:
Dear All
I have generated the INP.itp from tppmktop.
The INPt.itp file is:
; Topology was prepared for use with the force field:
; OPLS-AA revision jun16
; Please include ffoplsaa.itp into .top file
#ifndef TPPREV_jun16
#error CORRECT VERSION
I used the CGenFF program for generating the ligand topology. The GROMACS
tutorial recommends the manual reparameterization of force field in case
the penalty score exceeds 50. My ligand penalty scores exceed 50 and don't
know how to change the parameters. Please help in this regard. I am
Hi...you can use charmm gui...for generating the topology for a lipid by
layers.. it's much easier way to do...
On Wed 14 Aug, 2019, 12:28 PM Atila Petrosian,
wrote:
> Dear gromacs users,
>
> I want to do MD simulation of the lipid bilayer-ligand system.
> I used MD topology file from Automated
Dear gromacs users,
I want to do MD simulation of the lipid bilayer-ligand system.
I used MD topology file from Automated Topology Builder (ATB). ATB got
GROMACS G54A7FF United-Atom (ITP file) for ligand molecule.
How to get appropriate topology files for lipid bilayer?
Please guide me about
