Dear Girish,
It looks like that, even when using gaff, there are missing FF 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
either you continue to use gaff and add in the frcmod file the missing
FF parameters by analogy to existing ones; or you decide to use the
last update of parm99.dat and create by yourself the frcmod file.
I did not check in gaff.dat and parm99.dat but my guess is that the
van der Waals parameters for sy in gaff and S in parm99.dat derive all
from the Cornell et al. FF. Considering that your molecules is mainly
a peptide, I would use the last adaptation of the Cornell et al. FF
and not GAFF.
Personally, I prefer to manually create the frcmod file because you
better control what you do...
regards, Francois
> 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 Fri Jan 04 2013 - 06:30:03 PST
