答复: How to build the psf file and the parameter file of a ligand

From: Yu Liu (yliu452_at_uwo.ca)
Date: Mon Jul 16 2007 - 08:32:16 CDT

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Hi, you need find right CHARMM parameter files (for example
top_all27_prot_lipid.inp) and use the command “psfgen” to get your PSF
file. For more details, you can find from the tutorial files. I guess it is
in the chapter 1.2. By the way, you need to replace the alias name for some
atoms.

William Liu

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发送时间: 2007年7月16日 4:09
收件人: namd-l_ks.uiuc.edu
主题: namd-l: How to build the psf file and the parameter file of a ligand

Hi, all

I want to run a MD of a protein-ligand complex with NAMD. But I don't know
how to build the

 psf file and the parameter file of the ligand in the system. I have never
done it. What should

I do? Is there any plugin or soft that can generate the files and how?

Can anybody give me some advises? Thanks

Paul Tao

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