RE: problem at applying patch

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Aug 28 2010 - 13:21:14 CDT

A better way to do this would be to use the extraBonds feature in NAMD 2.7.
For some reason, it doesn't seem to be documented yet in the manual, but you
can see a previous post about it here:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7735.html (angles,
etc. are written similar to the bond example given).

 

 

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Kwee Hong
Sent: Saturday, August 28, 2010 12:58 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: problem at applying patch

 

Hi,

I was trying to add an angle to my system. In my script of generating the
appropriate pdb and psf, I added these line:

patch ANG B:102 A:24 B:104
patch ANG B:104 A:7 B:103
patch ANG B:103 A:15 B:102

where 102, 103 and 104 are respectively the residue no for 3 cadmium ions
which is coordinated by 2 deprotonated cysteines with residue number 7, 15,
24.

In my parameter file, I added this:

PRES ANG 0.00
ANGLE 1CAD 2SG 3CAD

But when I source the script in vmd TkConsole, I got this warning which I
don't understand why:

applying patch ANG to 3 residues
no atom CAD in residue CYB:24 of segment A
Warning: add angle failed in patch ANG
applying patch ANG to 3 residues
no atom CAD in residue CYB:7 of segment A
Warning: add angle failed in patch ANG
applying patch ANG to 3 residues
no atom CAD in residue CYB:15 of segment A
Warning: add angle failed in patch ANG

Can someone explain this to me? And how can I get this solved.

Thanks.

Regards,
Joyce

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