[gmx-users] RE: ATP TOPOLOGIES

Spiwok Vojtech Vojtech.Spiwok at vscht.cz
Tue Dec 16 12:35:01 CET 2003

>Raj Badhan :
>Does anyone have a working topology of ATP which has NOT been 
>created using PRODRG?
>My ATP from PRODRG seems to not like my simulations and I 
>would like to try another version of it. Sadly, I am a novice at 
>gromacs and am hvaing problems creating my own topologies.
>Thanks for the understanding and advice from David and others.

Did you check a protonation state on adenine ring? PRODRG usualy
adds one hydrogen on N-1 of adenine (by mistake). It could be
fixed by puting DELHYD + atomname of N-1 at the end of input PDB
file (see FAQ of PRODRG). Charges must also be inspected. PRODRG
assigns diferent charges to phosphate oxygens (probabily as P-O
and P=O). Also angles and improper dihedrals of phosphate group
must be inspected, but I used it only for docking, not MD, so I
didn't have to fix this.

>Raj Badhan
>Postgraduate researcher
>School of Pharmacy and Pharmacetical Science
>The University of Manchester
>Manchester, UK.

Good luck
Vojtech Spiwok
ICT Prague

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