[gmx-users] PRODRG warning
Andrew Horsfield
horsfield at fecit.co.uk
Wed Jan 16 16:05:21 CET 2002
Hi Daan,
> ???? I am confused now. You should feed the PRODRG output GMX topology
> *AND* PRODRG output PDB file into GMX? How else would GMX be able to
> correlate atom names in the topology with atom names in the PDB file?
I also modified the topology file. It starts:
[ atoms ]
; nr type resnr resid atom cgnr charge
1 H 1 MYP HA 1 0.000
2 NR6* 1 MYP N1 2 0.000
3 CB 1 MYP C1 3 0.380
4 O 1 MYP O1 3 -0.380
5 CB 1 MYP C2 4 0.000
6 NR6 1 MYP N2 5 0.000
7 CR61 1 MYP C3 6 0.000
8 CR61 1 MYP C4 7 0.000
9 NR6 1 MYP N3 8 0.000
10 CB 1 MYP C5 9 0.000
11 NR6 1 MYP N4 10 0.000
12 CB 1 MYP C6 11 0.000
13 NT 1 MYP N5 12 -0.830
14 H 1 MYP HC 12 0.415
15 H 1 MYP HB 12 0.415
On Wed, 16 Jan 2002, Daan van Aalten wrote:
> >???? I am confused now. You should feed the PRODRG output GMX topology
> >*AND* PRODRG output PDB file into GMX? How else would GMX be able to
> >correlate atom names in the topology with atom names in the PDB file?
>
> that pdb file still misses the residue number which confuses prodrg.
> Furthermore the output force constants are in kcal and Angstrom rather
> than kJ and nm.
I think is the resolution of the problem ...
Cheers,
Andrew
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