VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Aug 22 2006 - 10:12:45 CDT

Dear Sukesh,
if you want to make a chain with no terminal patching, you need to say
that in your chain block, eg

segment A {
pdb men.pdb
first NONE
last NONE
}

This is because most topology files define the default patches first
NTER last CTER.

Peter

Shenoy, Sukesh wrote:
> 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
>