From: Payal Chatterjee (payalchatterjee242_at_gmail.com)
Date: Wed Oct 28 2015 - 03:08:16 CDT
Dear Abhishek
Why don't you use charmm-gui for the same? Prepare the mol2 file for the
ligand, and you will get its parameter files. It is also one of the most
reliable sources of system preparation.
Thanks
Payal
On Tue, Oct 27, 2015 at 11:59 PM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
wrote:
> Dear Nikhil,
>
>
> Have you done tutorials available in NAMD. It will give you all idea about
> how to use all these files, and using swissparam server is not good idea
> you may use VMD to build your files. Have a look on mailing list experts
> have suggested many good ways.
>
>
> ABhi
>
>
>
>
>
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Nikhil Maroli <scinikhil_at_gmail.com>
> *Sent:* Wednesday, October 28, 2015 2:52 PM
> *To:* namd-l_at_ks.uiuc.edu; Vmd L
> *Subject:* namd-l: Including two parameters for protein-ligand simulation
>
> Dear all,
>
>
> i wanted to MD after docking i made psf file for ligand using swissparam
> server i got ligand.rtf file
> using script i made combined psf for the protein+ligand
>
> package require psfgen
> resetpsf
> topology top_all36_prot.rtf
> topology rutin2.rtf
> pdbalias residue HIS HSE
> segment A {
> pdb Ach.pdb
> first NTER
> last CTER
> }
> coordpdb Ach.pdb A
> guesscoord
> segment B {
> pdb rutin.pdb
> first NONE
> last NONE
> }
> coordpdb rutin.pdb B
> regenerate angles dihedrals
> writepsf new.psf
> writepdb new.pdb
>
> now i wanted to do MD for that i have to include the parameter files i
> have par_all27_prot_lipid.inp .what i have to do for ligand ?
> from server i got ligand.par as parameter file how i include that in namd
> configuration file?
>
> im posting this in both namd and vmd-l as it come under both
>
>
>
>
> --
> Ragards,
> Nikhil Maroli
>
>
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