VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Fri Mar 02 2007 - 12:41:59 CST

Dear Grazia,

In the topology file there should be a list of atom names and types and
below that, after the keyword BOND a list of atom name pairs that define
the bonds. In the same manner ther should be entries for ANGLE, DIHED
and if you have impropers also for IMPR.

If you send me your example files I can take a look at it and see if
something is wrong.

Jan

Grazia Daminelli schrieb:
> Hello
>
> I want to generate the internal coordinates of my system, starting from
> the pdb file and using paratool. I am loading my structure as "base
> molecule" and then asking paratool to autogenerate the internal
> coordinates. Bonds, angles, dihedrals are generated correctly, improper
> bonds are missing, so after picking the appropriate atoms I generate
> them with the "add coordinate" facility. In order to save the internal
> coordinates table in a file, I use the command "write topology file".
> But the values written in the topology file do not correspond to the IC
> values I can read in the "internal coordinate" windows and the IC
> improper are just missing. What happens during the writing of the
> topology file? Which values are written there?
>
> Thanks for your help
>
> Grazia
>
>
>
> 

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de