[AMBER] Structured water molecules with leap

From: Guenegou, Guillaume [ORDFR] <GGUENEGO.ITS.JNJ.com>
Date: Fri, 10 Jun 2011 15:39:48 +0200

Dear all,

I work with amber11 and AmberTools1.5.

I generate topology files with tleap. I have one protein, one cofactor
and one ligand.
I want to consider structured water molecules got by critallography.
I try something like the following input file but after some trials, I
am sure the solvatation (solvateBox ...) removes my structured water

Is there a way to keep them in the complex and to solvate the complex
with water?

cat > leap.in << EOF
source ${FORCEFIELD}
source leaprc.gaff
frcmod1 = loadamberparams ${COFACTOR}.frcmod
frcmod2 = loadamberparams ${LIG}.frcmod
prot = loadPdb ${INPUTDIR}/protein/${PROT}.pdb
cof = loadMol2 ${COFACTOR}.mol2
lig = loadMol2 ${LIG}.mol2
wat = loadPdb water.pdb
complex1 = combine {prot cof lig}
saveAmberParm complex1 ${PROT}_${LIG}.top ${PROT}_${LIG}.crd
saveAmberParm lig ${LIG}.top ${LIG}.crd
savePdb complex1 ${PROT}_${LIG}.pdb
complex4 = combine {complex1 wat}
addIons2 complex4 Na+ 0
addIons2 complex4 Cl- 0
solvateBox complex4 ${SOLVATEBOX} ${SOLVATECUT}
saveAmberParm complex4 ${FILE}.top ${FILE}.crd
savePdb complex4 ${FILE}.pdb
complex3 = combine {prot cof}
saveAmberParm complex3 ${PROT}.top ${PROT}.crd
savePdb complex3 ${PROT}.pdb


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Received on Fri Jun 10 2011 - 07:00:03 PDT
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