[gmx-users] *.ITP file

Kowsar Bagherzadeh kw_bagherzadeh at yahoo.com
Sun May 13 11:54:42 CEST 2012

 Dear Users,
 I am trying to generate an *.ITP file for a ligand I am studying using Prodrg server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar hydrogens) while the *.ITP file dispays 37 atoms and it does not display the double bond in the structure, which results in an error in simulation. Other files that Prodrg gives like DRGAPH.PDB display 37 atoms same as the *.ITP file and they also do not display the double bond in the structure ! only the DRGFIN.PDB with 41 atoms ( all hydrogens) displays the double bond. I have used Prodrg several times before and this is the first time it happens. are there any other online services or any software for the purpose? Thank you
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