[gmx-users] PRODRG warning

[Andrew Horsfield]

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