psfgen: creating segments without extra hydrogens?

From: Emerson Macedo (
Date: Sat Aug 13 2016 - 13:58:49 CDT

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,


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