Dear all,
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
Thanks in advance,
Brandon
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Received on Mon Jun 18 2012 - 12:00:03 PDT
