Dear all,
i wanted to include position restrain to cyclic peptide nanotube c-alpha
atoms,i have generated posre_cpn.itp file and added
define = -DPOSRES
in mdp file.
and added in .top as
#ifdef POSRES_Protein
#include "posre_cpn.itp"
#endif
when i check with gmx energy i couldnt find an
Thank you very much Dr. Lemkul
Sent from my iPhone
> On 02-Apr-2016, at 10:34 pm, Justin Lemkul wrote:
>
>
>
>> On 4/2/16 2:11 AM, sun wrote:
>> Hello Gromacs Users I have already posted this query but in the absence of
>> any suggestion, I am posting it again. I hope someone will help me. I
On 4/17/16 12:42 PM, REMYA R wrote:
Yes sir, even though its not working
You're going to have to provide a more complete explanation of what you're
doing. What steps you took, .mdp files, how you generated the ligand topology,
etc. Simply saying that the system crashed is inadequate to g
Yes sir, even though its not working
On Sun, Apr 17, 2016 at 9:41 PM, Justin Lemkul wrote:
>
>
> On 4/17/16 11:35 AM, REMYA R wrote:
>
>> Dear sir,
>>
>> I am getting error while running simulation of Protein-Ligand complex ,
>> usong GROMOS force field, spc water model at the equilibration p
On 4/17/16 11:35 AM, REMYA R wrote:
Dear sir,
I am getting error while running simulation of Protein-Ligand complex ,
usong GROMOS force field, spc water model at the equilibration phase of
bevan lab tutorial for protein-ligand simulation, version 4.6.1 (
http://www.bevanlab.biochem.vt.edu/P
On 4/17/16 12:05 AM, Shahla Omidi wrote:
​hello
I want to simulate my protein with charmm36, and I used gromacs505 for this
I took this error with pdb2gmx
"Residue 1 named PRO of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction
On 4/17/16 3:58 AM, Patricia Jones wrote:
Hello Dear Users
I am using Gromacs 5.0 for protein-ligand simulation. After completing 50
ns MD following Justin's tutorial, I have used gmx_mdmat for protein
residue contact matrix. Now, I want to use this command for protein-ligand
atom contacts. Is
Dear sir,
I am getting error while running simulation of Protein-Ligand complex ,
usong GROMOS force field, spc water model at the equilibration phase of
bevan lab tutorial for protein-ligand simulation, version 4.6.1 (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl
Hello Dear Users
I am using Gromacs 5.0 for protein-ligand simulation. After completing 50
ns MD following Justin's tutorial, I have used gmx_mdmat for protein
residue contact matrix. Now, I want to use this command for protein-ligand
atom contacts. Is this possible using mdmat? or is there any ot