[gmx-users] PRODRG Server

[hugo verli]

Hi to all,

I'm using the PRODRG Server to generate topologies for a poly-sulphated and
poly-carboxylated compound. The total charge is about -12. However, the PRODRG
Server did not recognize the system charge:

PRODRG> 105 atoms read.
PRODRG>  10 hydrogens added
PRODRG> 120 bonds               50 ambiguous
PRODRG> 187 bond angles        142 ambiguous
PRODRG>  44 improper dihedrals   0 ambiguous
PRODRG>  77 dihedrals           26 ambiguous
PRODRG>  79 partial charges     52 ambiguous
PRODRG> Net charge on molecule :   0.000

In the topology file the oxygen atoms of sulphate groups have zero charge, as
well as the sulphur atom. Is this what I should expect from the Server? 

The replacement of these charges by semi-empirical or ab-initio charges would
create some kind of problem with the forcefield parameters? i.e. is this the
right choice to represent the electrostatic properties of these molecules?

One more question. I have inserted another molecule of 210 atoms in PRODRG
Server. I received the following message:

ERRDRG> Error in recursion (molecule too complex).
PRODRG> Drug topology not made, sorry!

The pdb file is ok. Am I missing something?


Thanks in advance for any kind of help,

Hugo Verli.