VMD-L Mailing List

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Tue Aug 22 2006 - 12:41:51 CDT

Hi, I can see a couple issues with your residue:

Each group must be unit charged. From the documentation (rtop.doc):

Designation of the various residues, nucleotides etc. is done
using the (G) RESIdue keyword followed by the residue name (four
characters) and the total charge of the residue. A residue may then
be subdivided into (G1) GROUps, which contain several atoms whose total
charge is neutral or a unit charge.

You do not have a bond between the methyl carbon and the nitrogen.

There are other strange things going on here; I suggest that you
examine rtop.doc and the topology libraries in
order to make sure that you are setting things up consistently and
correctly.

Cheers,

Mike
On Aug 21, 2006, at 3:41 PM, Shenoy, Sukesh wrote:

> 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
> 

--
C. Michael McCallum           http://www.pacific.edu/college/ 
chemistry/McCallum/cmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax