You can generate the psf file using VMD, either with psfgen or autopsf
(gui). The basic NAMD tutorial is located here and has a section of
building the psf:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/namd-tutorial-unix.html
On Thu, Mar 9, 2017 at 4:56 AM, Shanghaitech University WuMeng <
wumeng.shanghaitech.edu.cn> wrote:
> Hi All,
>
> I am running a membrane protein MD simulation with Amber16. I want to
> use the chamber tools in parmed to set CHARMM36 parameters for my system,
> but I am trapped with a problem:
> Is there a way to generate psf file from pdb file which is actually a
> protein ligand complex and lipids in water box and if it is so, then how?
> Maybe I can use Charmm-gui more directly, but the protein is not mine...
>
> Any suggestions would be greatly appreciated. Thank you in advance!
>
> All the best,
> Wu Meng
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Thu Mar 09 2017 - 09:30:02 PST
