Dear Jason,
I would like to know one thing if I source leaprc.ff99SBildn, how i should
proceed
Is it like this? I have followed the amber tutorial
http://ambermd.org/tutorials/basic/tutorial4b/.
should I also apply leaprc.ff99SBildn in case of ligand also?
tleap -f leaprc.ff99SBildn
>source leaprc.gaff
I am giving you the details.
*for ligand*
antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
*$tleap -f leaprc.ff99SB*
*source leaprc.gaff*
SUS = loadmol2 sustiva.mol2
check SUS
loadamberparams sustiva.frcmod
saveoff SUS sus.lib
saveamberparm SUS sustiva.prmtop sustiva.inpcrd
*for pdb + ligand*
*tleap -f leaprc.ff99SB*
*>source leaprc.gaff *
>loadamberparams sustiva.frcmod
loadoff sus.lib
>complex = loadpdb 1FKO_trunc_sus.pdb
>saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd
>savepdb complex 1FKO_sus.pdb
>quit
Thanks in advance
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Received on Wed Oct 09 2013 - 07:30:04 PDT
