[gmx-users] PRODRG Server

[Nguyen Hoang Phuong]

> 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? 


I also had the same problem with my peptide and according to D.M.F. van
Aalten, usually the charge is not perfect and one has to change the value
of charge in the top file by hand.

> 
> 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?

this I do not know, sorry!
> 
> 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?

I think the sever can only convert the pdb file of small molecules to the
topology file. Perhaps, your molecule is big.
  

> 
> 
> Thanks in advance for any kind of help,
> 
> Hugo Verli.
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