Hi,
I'm trying to parametrise some of the HIV-1 protease inhibitors and am
having a problem with TMC-126.
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=17396648
I used the RESP methodology to generate the partial charges via the RED
program using 6-31G* basis set. Using antechamber in AMBER 10, I generated
a mol2 file and used parmchk to create a frcmod file. The latter is as
follows:
$AMBERHOME/exe/antechamber -i Mol_m1-o1.mol2 -fi mol2 -o TMC-126.mol2 -fo
mol2 -s 2
parmchk -i TMC-126.mol2 -o frcmod
###################
remark goes here
MASS
BOND
n3-sy 353.80 1.632 same as n3-s6
ANGLE
c3-n3-sy 63.900 115.810 same as c3-n3-s6
n3-sy-o 72.900 106.800 same as n3-s6-o
n3-sy-ca 39.678 103.680 Calculated with empirical approach
DIHE
IMPROPER
n -o -c -os 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
ca-ca-ca-ha 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
ca-ca-ca-sy 1.1 180.0 2.0 Using default
value
ca-ca-ca-os 1.1 180.0 2.0 Using default
value
NONBON
###################
After creating the library file, when I try to create the topology and
co-ordinate files to run a test simulation, the process fails.
The commands are:
########## Commands #####
source leaprc.gaff
#source leaprc.ff03.r1
loadoff TMC-126_final.lib
savepdb DJR DJR_ligand_unsolvated.pdb
mol = loadpdb DJR_ligand_unsolvated.pdb
solvatebox mol TIP3PBOX 10.0 0.4
charge mol
savepdb mol DJR_ligand_SOLVATED.pdb
saveamberparm mol DJR_ligand.parm DJR_ligand.crd
charge mol
#########################
The output as follows
########## Output#####
-I: Adding /apps/applications/amber/10/1/default/dat/leap/prep to search
path.
-I: Adding /apps/applications/amber/10/1/default/dat/leap/lib to search
path.
-I: Adding /apps/applications/amber/10/1/default/dat/leap/parm to search
path.
-I: Adding /apps/applications/amber/10/1/default/dat/leap/cmd to search
path.
-f: Source ligand.tleap.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./ligand.tleap
----- Source: /apps/applications/amber/10/1/default/dat/leap/cmd/leaprc.gaff
----- Source of
/apps/applications/amber/10/1/default/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters:
/apps/applications/amber/10/1/default/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
Loading library: ./TMC-126_final.lib
Writing pdb file: DJR_ligand_unsolvated.pdb
Loading PDB file: ./DJR_ligand_unsolvated.pdb
total atoms in file: 77
solvateBox: Argument #2 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
Total unperturbed charge: -0.000300
Total perturbed charge: -0.000300
Writing pdb file: DJR_ligand_SOLVATED.pdb
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: n3 - sy
Building angle parameters.
Could not find angle parameter: c3 - n3 - sy
Could not find angle parameter: n3 - sy - o
Could not find angle parameter: n3 - sy - o
Could not find angle parameter: n3 - sy - ca
Could not find angle parameter: c3 - n3 - sy
Building proper torsion parameters.
Building improper torsion parameters.
total 12 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
Total unperturbed charge: -0.000300
Total perturbed charge: -0.000300
#########################
I don't know all the details of parmchk, but is the issue seems to to do
with the the sy atom type not being recognised. I thought that the second
column would reference the correct name. i.e. "same as c3-n3-s6".
* If I manually change the sy atom type to s6 in the mol2 file created by
antechamber, the mall the errors bar one dissapear:
### output ####
Could not find angle parameter: n3 - s6 - ca
Building proper torsion parameters.
Building improper torsion parameters.
total 12 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
################
If anyone could offer any advice on how to solve this issue, I would be
most grateful.
Best regards,
gt
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Received on Thu Jan 03 2013 - 17:00:02 PST
