Hi there,
I just tried to create parameters for GDP and GTP using antechamber (Amber 7).
Everything sort of worked but antechamber seemed to not only ignore the
"-nc -3" parameter but actually assigned charge 0.0 to all atoms.
It's the first time that I am using it, perhaps I made some obvious mistake.
Here is the command:
antechamber -i GDP_in.pdb -fi pdb -o GDP.prep -fo prepi -nc -3 -rn GDP -at
amber -c resp
GDP_in.pdb was prepared from the X-ray structure. I deleted the addidtional P,
added hydrogens in tleap and added back the P.
parmchk -i GDP.prep -f prepi -o frcmod.gdp
gives a frcmod in which some bond angles are marked as missing, although they
are existing in the parm99.dat. I just copied them over from parm99.dat.
tleap loads the prep and then the PDB without trouble but all the atoms have 0
charge. Any ideas anyone, what could have gone wrong?
Or alternatively, has anyone already parameters ready for GDP / GTP?
Many thanks!
Raik
-----------------------------------------------------
Raik Grünberg | Bioinformatique Structurale
| Institut Pasteur
Tel: +33/1.45.68.87.37 | Paris, France
-----------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed May 05 2004 - 21:53:00 PDT
