Re: psfgen: creating segments without extra hydrogens?

From: Brian Radak (
Date: Sun Aug 14 2016 - 16:39:59 CDT

The commands you describe build off of a residue template defined from
the topology file. Since those templates contain hydrogens, the
resulting structure must also have hydrogens.

If you do not want hydrogens, then use a template that does not include
them. I don't have any experience with united atom force fields in RTF
format, but I would not be surprised if they exist.



On 08/13/2016 01:58 PM, Emerson Macedo wrote:
> Hello NAMD experts!!
> I have a doubt about generating psf files for NAMD use.
> Is it possible to do that without psfgen?
> I'll explain.
> When using psfgen as shown in NAMD/VMD tutorials, 2 commands are
> normally used: segment and coordpdb.
> The segment command created the necessary segment and also inserts
> extra hydrogen atoms in the segment.
> Here it is my real problem:I want to create the segment without these
> extra hydrogens and use the coordpdb command. But, coordpdb does not
> work without segment created right before with the segment command.
> I tried that. I created the segment I wanted without the hydrogens,
> omitted the segment command and it didn't work, because the coordpdb
> did not recognized the segment I've created because (i guess)it needs
> the segment command to be executed before.
> Any directions would be very much appreciated.
> Thank you all for any help.
> Best regards,
> Emerson

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:22 CST