Dear Justin and Mark,
I also need to impose a distance restraints between COM of protein active
site residues and COM of a ligand. But the problem is I am using an .itp
file generated from acpype. While I use it externally I can not impose the
distance restraints between the protein and the ligand
Dear Mark,
I also identified that there is no improper dihedral terms produced for the
ligand by pdb2gmx I checked top file , it has all proper dihedral terms
defined but only thing is that manual intervention to change the function
type from 9 to 3 but I have defined all improper in ffbonded.i
Thank you Mark, I will workout your suggestions.
Regards,
Raja
On May 12, 2015 8:50 PM, "Mark Abraham" wrote:
> Hi,
>
> I don't know if that particular functionality is supported, but if you look
> at the way the GROMOS force fields implement their parameter lookups, you
> can see that
>
> [dihed
Hi,
I don't know if that particular functionality is supported, but if you look
at the way the GROMOS force fields implement their parameter lookups, you
can see that
[dihedral]
N C C O phi kphi mult
just works, presumably by generating the default dihedraltype. You can only
try
[dihedral]
N C
Thanks Mark, right now I am identifying the dihedral of ligand atoms in top
file produced by pdb2gmx and replace the function type from default 9 to 3
and so the grompp process the new dihedral defined in the ffbonded.itp
successfully. But I would like to identify a straight solution that pdb2gmx
t
Hi,
Another way to unite two .itp files is to write a script to renumber all
the atom indices in the second molecule's .itp so that they follow on from
those in the first molecule. Then you can cut and paste them together.
Mark
On Tue, May 12, 2015 at 3:56 PM Raj D wrote:
> Dear Justin,
> Than
Dear Justin,
Thanks ,I am doing it to bring the ligand and protein under one molecule
type in order to apply distance restraint between atoms of ligand and amino
acids . This I am doing based on your suggestion for my earlier post
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-Ma
On 5/12/15 12:05 AM, Raj D wrote:
Dear User,
I have done MD simulation successfully with ligand.itp file produced by
Antechamber. Now I have to include the ff information of the ligand into
AMBER99SB forcefield
and in the process I am so for successful in creating rtp entry and bond
and angles
Dear User,
I have done MD simulation successfully with ligand.itp file produced by
Antechamber. Now I have to include the ff information of the ligand into
AMBER99SB forcefield
and in the process I am so for successful in creating rtp entry and bond
and angles parameter in ffbonded.itp file but I h
