[gmx-users] FAD containing protein

[Andrea Carotti]

Hi all,
    I'm new with this kind of problems.I'll show what I've done:
i've changed my pdb atom types and residue name of FAD in FMN + ATP (taking
this information from the thesis of Anton Feenstra and vieweng the
ffG43a1.rtp)..but I've encountered this problems doing:
pdb2gmx -f xxx.pdb -o -p -ignh -->Gromos (official dist)--> Error: missing
atoms (infact I'm using the ATP for the residue name, but I've a AMP and it
didn't find PB and PG + oxygens....so i've run:
pdb2gmx -f xxx.pdb -o -p -ignh -missing ---> Error: atom name AO3PB non
found in residue ATP 498 while generating exclusions
Now I don't know what else I can do...
Please someone could help me
Thanks
Andrea
PS: I'm using gmx 3.2.1

------------
Andrea Carotti
Dip. Farmaco-chimico (Università di Bari)
via E. Orabona, 4 ## CAP 70124 ## BARI (Italy)
web: http://www.farmchim.uniba.it/samba/
phone: (+39) 080 5442551  ##   fax: (+39) 080 5442230