Dear Brandon,
If you look at the "F-90" R.E.DD.B. project, you will find GMP, GDP,
GTP and far more...
see
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
read the script:
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
modify it according to the files available in this project & simply
run it: tleap -f script1.ff
regards, Francois
> I have searched through the AMBER archives already for a solution to this
> problem, but I'm still unsure of how to address this issue:
>
> I am trying to model GDP using AMBER, but I am having trouble using
> antechamber. I am familiar with the GDP/GTP parameters located at
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box, but I am assuming
> (though I may be incorrect) that I still have to run antechamber on my GDP
> molecule in order to generate a .mol2 file to load into a library for
> further minimisation, etc. To perform minimisation and further simulations
> involving GDP in complex with other molecules, do I indeed need to generate
> the .mol2 file, etc?
>
> If so, then -
>
> The error that I encounter is the odd electron problem:
>
> Total number of electrons: 227; net charge: -2
> INFO: Number of electrons is odd: 227
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
> The input PDB file I am using is attached. I have specified a net charge of
> -2 in my command:
>
> $AMBERHOME/bin/antechamber -i GDP_2.pdb -fi pdb -o GDP.mol2 -fo mol2 -c bcc
> -s 2 -nc -2
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Received on Mon Jun 18 2012 - 16:00:03 PDT
