AMBER Archive (2006)

Subject: AMBER: Charges on atoms in protein :AMBER

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Wed Feb 01 2006 - 21:00:09 CST

Hello,
I generated pdb file after runnig leap:

My leap.in is

source leaprc.gaff
source leaprc.ff99
loadoff ZNC.lib
loadoff HIC.lib
loadoff HIF.lib
loadoff wat.lib
loadAmberParams frcmod.caii
loadAmberParams frcmod.znc
loadAmberParams ligand.frcmod
loadAmberprep HIC.in
loadAmberprep wat.in
loadAmberprep ligand.prepin
loadAmberprep HIF.in
set BZO restype protein
set ZNC restype protein
set HIC restype protein
set HIF restype protein
Prot = loadPdb protein.pdb
charge Prot
addions Prot K+ 1
solvateBox Prot TIP3PBOX 12 iso
saveAmberParm Prot prmtop.top prmcrd.crd
savepdb Prot protein-mod.pdb
check Prot
charge Prot

But when i look at structure in Sybyl7.1 and try to
display charge on residues i see 0.0 charge on every
single atom. Does amber assign charge by itself or do
we assign charges to residues before running leap.

Thanks in advance,
Varsha Gupta

        

        
                
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