VMD-L Mailing List

From: Shenoy, Sukesh (sukeshshenoy_at_neo.tamu.edu)
Date: Tue Aug 22 2006 - 10:03:41 CDT

Howdy,

When i use psfgen to generate the psf file for methyl nitrate whose
structure is given below, it adds a default NTER and CTER. Also says that
atom C not found in residue MEN:1.
     I would be grateful if somebody could help me with this.

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
PATCHING FIRST NONE LAST NONE

Thanks,
Sukesh