Dear all,
I am trying to compile IED (Interactive essential dynamics) according to the
instructions of
http://mccammon.ucsd.edu/ied/
However, I always got such errors:
--
vmd > gopython
Info) Starting Python...
Traceback (most recent call last):
File "",
?Dear Gromacs users,
When running grompp to create 'ions.tpr' file for energy minimisation of a
protein-ligand complex (following the protein-ligand complex tutorial), I am
getting the error:
ERROR 1 [file mNEP2.top, line 19069]:
atom C2 (Res LIG-1) has mass 0 (state A) / 0 (state B)
Atom
Hi, Prakash：
you can try mdtraj.
http://mdtraj.org/1.8.0/examples/native-contact.html
Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn *
On Fri, Apr 28, 2017 at 6:19
Dear all,
I need to calculate fraction of native contacts as a measure of protein
denaturation. Please suggest ways to do so in Gromacs. I tried to use
mdmat. Is there a better tool?
Regards,
Prakash.
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Hi,
I'm following Umbrella sampling tutorial of gromacs. But it was going all
fine since I hit an issue with my system.
I had minimized my system well. But when I started the NPT equilibration it
is giving me: pressure scaling more than 1%
It says, probably the system is not equilibrated/minimized
