Problems of assigning the right atom types in antechamber


new in xleap.sh (29.04.2005):
The local file my_ATOMTYPE_GFF.DEF is used for changing atom types in prep-files of antechamber:
antechamber -i $ligand2 -fi pdb -a $sdf -fa mdl -ao bond -j 5 -o PREP_AC.AC -fo ac -c bcc -rn $ligandname -nc $charge -pf y
atomtype -i PREP_AC.AC -o PREP_TYPE.AC -d $atomtypegff
prepgen -i PREP_TYPE.AC -o $prep -f int -rn $ligandname
modification in my_ATOMTYPE_GFF.DEF for guanidino group attached to armoatic rings:
//SH 22.04.05 for guanidino group attached to aromatic ring (1ejn)
// /-\ /nb
// ca-nb-ca
// \_/ \nb
ATD nb * 7 3 1 * * (C3[AR1],C3(N3,N3))
ATD nb * 7 3 2 * * (C3(N3,N3(C3[AR1])))
ATD ca * 6 3 0 * * (N3(C3[AR1]),N3,N3)

modification in my_ATOMTYPE_GFF.DEF for guanidino group involved in ring attached to aromatic ring:
//SH 28.04.05 for guanidino group involved in ring attached to aromatic ring (1sqo)
// /cc-cc\ /nb-c2\
// cc cd-na-c2 c2
// \c2-cc/ \nb-c2/
ATD nb * 7 3 1 * [AR3] (C3[AR3],C3[AR3](N3,N3))

the files for the following examples can be downloaded by using URL http://projects.villa-bosch.de/mcm/projects/tassfun/reports/antechamber_problems/ + filename

first example (1o2k)

antechamber + parmchk with: lig.ligand.pdb
output: lig.parm + lig.top

tleap -f lig.xleap.script
input:
lig.modifnew.pdb
lig.parm + lig.prep
extra.lib
output:
lig.xleap.pdb
lig.top
lig.cor

sander:
lig.protmin.restrain.in
output:
lig.min.xyz
lig.min.pdb

nitrogens N1 and N2 after minimization not planar!

modification in ATOMTYPE_GFF.DEF:
ATD na * 7 3 * * [AR1.AR2.AR3]
ATD na * 7 3 * * * (C3(N3,C3[AR1.AR2.AR3]))

and reading added_ligand.parm, extra.lib also in tleap the minimized ligand looks better:

antechamber + parmchk with: lig.ligand.pdb
output: lig.mod.parm + lig.mod.top

tleap -f lig.mod.xleap.script
input:
lig.mod.modifnew.pdb
lig.mod.parm + lig.mod.prep
extra.lib
output:
lig.mod.xleap.pdb
lig.mod.top
lig.mod.cor

sander:
lig.protmin.restrain.in
output:
lig.mod.min.xyz
lig.mod.min.pdb

second example (1f5l)

modification in ATOMTYPE_GFF.DEF:
ATD na * 7 3 * * [AR1.AR2.AR3]
ATD na * 7 3 * * * (C3(N3,C3[AR1.AR2.AR3]))

antechamber -i lig2.ligand.pdb -fi pdb -o lig2.prep -fo prepi -c bcc -rn A26 -nc +1

parmchk -i lig2.prep -f prepi -o lig2.parm -p gaff.dat

tleap -f lig2.xleap.script

sander -O -i ./lig2.protmin.restrain.in -o ./lig2.min.out -p ./lig2.top -c ./lig2.cor -r ./lig2.min.xyz -ref ./lig2.cor

ambpdb -p ./lig2.top ./lig2.min.xyz ./lig2.min.pdb

C3 and all nitrogens are not planar after minimization. Better results after using the prep file: lig2.na-ca-C3ce.prep

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update: 29.04.2005

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