[gmx-users] Prodrg disturbed hybridization state of doubly bonded nitrogen

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 13 09:15:39 CET 2016

On 13/02/16 08:11, Saman Yousuf ali wrote:
> Dear all,I am a beginner here. I have prepared my ligand topology file using prodrg, it gave me the following error,
> PRODRG> Starting up PRODRG version AA100323.0717PRODRG> Parameter set 'pd/gromos96' (fftype=2).PRODRG> PDB mode detected.PRODRG> WARNING: deleted hydrogen(s) from your input.PRODRG> Molecule complexity index: 2.11.PRODRG> WARNING: applied 1 unusual hybridisation fixup(s).PRODRG> 13 hydrogen(s) added.PRODRG> Using charge groups.PRODRG> Net charge on molecule: 0.000PRODRG> 19 partial charges 1 ambiguousPRODRG> 33 bonds 10 ambiguousPRODRG> 55 bond angles 34 ambiguousPRODRG> 17 improper dihedrals 2 ambiguousPRODRG> 11 dihedrals 5 ambiguousPRODRG> Writing GROMACS topology.PRODRG> GROMACS topology quality on 0-10 scale: 5.8PRODRG> Keeping old coordinates.PRODRG> RMSD from GROMOS bond ideality (Angstrom) : 0.060PRODRG> RMSD from GROMOS angle ideality (degrees) : 5.631PRODRG> RMSD from GROMOS plane ideality (degrees) : 2.317PRODRG> Number of improper improper dihedrals : 0PRODRG> Writing: SCRTHOWMMPGPRODRG> Normal program end.
> Prodrg disturbed hybridization state of doubly bonded nitrogen atom and it remove double bond and attach hydrogen on this atom. Kindly suggest me how can I fix this problem.
> Thank you.

Your mail is unreadable and you do not mention the name of the molecule.
Unless there is a very strong reason to use the gromos force field you 
probably want to consider using Amber tools with the acpype tool to make 
a gromacs compatible topology, or Charmm with the CGENff tool.

>   Best Regards, Saman Yousuf AliJunior Research Fellow,
> | Lab No. P-133, Computational Chemistry Laboratory
> Dr. Panjwani Center for Molecular Medicine & Drug Research,
> International Center for Chemical & Biological Sciences,
> University of Karachi – 75270.Karachi-Pakistan.
> Contact No:
> Office (92-21) 111222292 (Ext 309)
> Email ID: saman.yousufali64 at yahoo.com
>   saman.ali at iccs.edu
>     |

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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