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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:28 CST