[gmx-users] PRODRG warning

[Daan van Aalten]

Hi Andrew

???? 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?

cheers

Daan



On Wed, 16 Jan 2002, Andrew Horsfield wrote:

> Hi Daan,
> 
> > One problem may be that your PDB file does not have proper atom names.
> > How can GMX know which "C" is "C" if they are all called "C"? You
> > might try it with C1 C2 C3 C4 etc. and see if that helps?
> 
> The PDB file I mailed to you goes only to PRODRG. The PDB file I fed to
> Gromacs (based on the PRODRG output) was:
> 
> ATOM      1  HA  MYP            -6.108  30.035  20.765
> ATOM      2  N1  MYP            -5.276  29.686  21.240
> ATOM      3  C1  MYP            -4.110  30.463  21.020
> ATOM      4  O1  MYP            -4.136  31.409  20.251
> ATOM      5  C2  MYP            -2.973  29.975  21.825
> ATOM      6  N2  MYP            -1.798  30.612  21.705
> ATOM      7  C3  MYP            -0.802  30.158  22.460
> ATOM      8  C4  MYP            -0.980  29.074  23.341
> ATOM      9  N3  MYP            -2.132  28.426  23.469
> ATOM     10  C5  MYP            -3.159  28.865  22.701
> ATOM     11  N4  MYP            -4.343  28.184  22.814
> ATOM     12  C6  MYP            -5.348  28.612  22.097
> ATOM     13  N5  MYP            -6.571  28.005  22.221
> ATOM     14  HC  MYP            -6.538  27.144  22.758
> ATOM     15  HB  MYP            -7.191  27.989  21.417
> 
> Does PRODRG also need unique identifiers?
> 
> Cheers,
> 
> Andrew
> 


##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

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