Hello Shahla,
We have developed a tool for GROMACS (rtp2hdb) that can construct a hdb table
file for you with any rtp file. Please contact me contact me off list if you
are interested
Best
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Message: 5
Date: Sat, 9 Apr 2016 08:49:05 -0400
From: Justin Lemkul
Hi,
i am following this method
(http://www.sciencedirect.com/science/article/pii/S0010465514002240)
so when i run the script it has to generate gro file for all the 1000
pdb's (100ns MD) , inserting *.itp and *.prm files will take lots of time
for each steps ;) ,i dont have knowledge in perl
Hi,
These tools are not intended to be deterministic. gmx genion -h etc. will
talk about random components, and how to seed them. Parallel mdrun is not
generally reproducible. But there is nothing useful to conclude from
several EM runs converging to the same structure.
Mark
On Sat, Apr 9, 2016
On 4/9/16 8:42 AM, Nikhil Maroli wrote:
Dear all,
i m doing mmpbsa calculation using GMXPBSA tool ,for protein ligand complex
during the steps i invoked the command
pdb2gmx -f _comp0.pdb -p topol_comp.top -i posre_comp.itp -o _comp0.gro
-ignh -water tip3p
i have generated the ligand
On 4/9/16 1:55 AM, Shahla Omidi wrote:
Hi
I want to simulate a glycoprotein, I have defined a new residue with charmm36
inorder to update the .hdb file, I need to define the order of atoms that are
conecting to atoms that is conecting to H atoms in my new residue
but I dont exactly know
Hi Tsjerk,
Thank you for your response. I notice that between replicates, the
number of water solvate reports is sometimes not exactly the same
(though not by much, for the same box size and geometry), and the Fmax
at which em gives up is also different (up to 50%), at a different
atom.
Dear all,
i m doing mmpbsa calculation using GMXPBSA tool ,for protein ligand complex
during the steps i invoked the command
pdb2gmx -f _comp0.pdb -p topol_comp.top -i posre_comp.itp -o _comp0.gro
-ignh -water tip3p
i have generated the ligand topology such as *.itp and *.prm file ,but it
