Re: Warnings of psfgen

From: Vishal Kopardé (vnk_sim_at_yahoo.co.uk)
Date: Wed Oct 25 2006 - 17:09:15 CDT

• Next message: Gaurav Sharma: "Question about ABF"
• Previous message: jonathan_at_ibt.unam.mx: "Re: Warnings of psfgen"
• In reply to: Vishal Kopardé: "Warnings of psfgen"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

I found this

And NAMD uses Charmm22 , so I think I have to change all terminal
group O/OXT to OT1/OT2, respectively. I manually changed the pdb file
and it stopped giving me the error.
Please let me know if I am correct about this.
Thanks,
V
On Oct 25, 2006, at 9:37 AM, Vishal Kopardé wrote:

> Hi All,
> During the making of the .psf file using psfgen I got these
> "warnings", what do they mean and whats their consequence:
> reading coordinates from pdb file frag7.pdb for segment I7
> Warning: failed to set coordinate for atom O ASN:21 I7
> Warning: failed to set coordinate for atom OXT ASN:21 I7
> I got these warnings consistently for the last two atoms in
> each protein fragment.
> Regards,
> Vishal
> p.s. complete psfgen output attached.
> <out2>

Send instant messages to your online friends http://uk.messenger.yahoo.com

• application/pdf attachment: pastedGraphic.pdf

• Next message: Gaurav Sharma: "Question about ABF"
• Previous message: jonathan_at_ibt.unam.mx: "Re: Warnings of psfgen"
• In reply to: Vishal Kopardé: "Warnings of psfgen"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:44 CST