Re: basic: combining two pdb files?

From: Luis Rosales (
Date: Fri Jun 24 2005 - 03:25:46 CDT

Hi Vincent,

See the Userguide... :P
just kidding!

Well, to do that and assuming that you have your psf and pdb files for each
molecule, you just run an script like this on vmd:
package require psfegen

readpsf file1.psf
readpsf file2.psf

coordpdb file1.pdb
coordpdb file2.pdb

writepsf all.psf
writepdb all.pdb

And Voilá!!! You are done...
Hope this helps, and sorry for the silly joke... :)


> Can anybody help:
> I have two different pdb files and I can generate the separate psf
> files for namd run. Now, a very basic question: how can I combine both
> molecules for a single namd simulation? Sorry if this sounds silly... but
I'm new on this.
> Vincent

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