VMD-L Mailing List

From: Shenoy, Sukesh (sukeshshenoy_at_neo.tamu.edu)
Date: Mon Aug 21 2006 - 17:41:52 CDT

Howdy,
     I am trying to generate the psf file for methyl nitrate using psfgen.
It gives me the following error.

Info: generating structure...
ERROR: Missing atoms for bond N(0) O1(0) in residue MEN:1
ERROR: Missing atoms for bond N(0) O3(0) in residue MEN:1
ERROR: Missing atoms for bond N(0) O2(0) in residue MEN:1
ERROR: Missing atoms for bond CB(0) O3(0) in residue MEN:1
ERROR: Missing atoms for bond CB(0) HB3(0) in residue MEN:1
ERROR: Missing atoms for bond CB(0) HB2(0) in residue MEN:1
ERROR: Missing atoms for bond CB(0) HB1(0) in residue MEN:1
no atom C in residue MEN:1 of segment U
Warning: add conformation failed in patch NTER
Info: segment complete.
reading coordinates from pdb file nitromethane.pdb for segment U
Warning: failed to set coordinate for atom CB MEN:1 U
Warning: failed to set coordinate for atom HB1 MEN:1 U
Warning: failed to set coordinate for atom HB2 MEN:1 U
Warning: failed to set coordinate for atom HB3 MEN:1 U
Warning: failed to set coordinate for atom O1 MEN:1 U
Warning: failed to set coordinate for atom O2 MEN:1 U
Warning: failed to set coordinate for atom O3 MEN:1 U

I tried to add a new residue to the topology file
Here is the text of the residue.

RESI MEN 0.00
GROUP
ATOM CB CT3 0.21 !
ATOM HB1 HA 0.00 !methyl nitrate
ATOM HB2 HA 0.00 !
ATOM HB3 HA 0.00 !
GROUP
ATOM N N 1.32
ATOM O1 O -0.57
ATOM O2 O -0.52
ATOM O3 O -0.44
BOND N O2 CB HB2 CB HB3
BOND CB O3 N O3 CB HB1
DOUBLE N O1
IC HB1 CB O3 N 1.0943 101.5661 -179.9875 117.5269 1.5226
IC HB2 CB O3 N 1.0959 112.4035 62.3384 117.5269 1.5226
IC O1 N O3 CB 1.1946 117.7188 -0.0169 117.5269 1.3991
IC O2 N O3 CB 1.1868 108.8277 -180.0136 117.5269 1.3991
IC HB3 CB O3 N 1.0959 112.4035 62.3384 117.5269 1.5226

can anyone please tell me how to solve this error?
Sukesh