On 4/6/14, 10:29 AM, Sanchaita Rajkhowa wrote:
Hii, I understand renaming the atoms in the coordinate file but how do I
do the one-to-one mapping of the atoms?? Which atom in the pdb file
represnt AP or AO5* in the forcefield file?
The N prefix indicates atoms belonging to the nicotinamide
Hii, I understand renaming the atoms in the coordinate file but how do I
do the one-to-one mapping of the atoms?? Which atom in the pdb file
represnt AP or AO5* in the forcefield file?
Atoms in gromos96 forcefield file-
[ NADH ]
[ atoms ]
AP P 0.76000 0
AO1POM-0.63500
On 4/6/14, 7:05 AM, delara aghaie wrote:
Dear Gromacs Users
I want to simulate human p53 protein and two of its mutants to see how mutation
affect its structural properties.
I obtained the nature and mutant pdb files form protein data bank.
when I submitted the mutant files to pdb2gmx command
Dear Gromacs Users
I want to simulate human p53 protein and two of its mutants to see how mutation
affect its structural properties.
I obtained the nature and mutant pdb files form protein data bank.
when I submitted the mutant files to pdb2gmx command it gave error on misiing
atoms. I fixed the
See following paper for modelling of initial steps of glycation process
protein:
http://www.tandfonline.com/doi/abs/10.1080/07391102.2010.10507354#preview
For study of advanced glycation end processes, there is nothing to do with
emperical FF,
you need to use QC approches;
see following papers fo
Hi Ahmet,
Nothing wrong with specbond at this point. The bonds are correctly added,
and apparently the bondtypes are read correctly too, because grompp only
starts complaining at the point of angles. Check the atomtypes
corresponding to the atoms involved in those angles in the .itp file that
is g
