[gmx-users] PRODRG Server
hugo at acd.ufrj.br
Thu Jul 25 22:40:46 CEST 2002
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,
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