problem at applying patch

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sat Aug 28 2010 - 12:58:21 CDT

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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