Dear Alan,
Thanks for the detailed information. I appreciate it.
Yes, I need to update my acpype version. Is there any way to print the
proper dihedral parameters by acpype?
root_GMX.itp contains the RB dihedral parameters.
Tarak
On Thu, Jan 14, 2016 at 2:43 PM, Alan <alanwilter.gmail.com> wrote:
> Dear Tarak, ACPYPE should work fine with GMX 4.5 (old GMX 4.0 had only RB
> option).
>
> Check if you using the last version of ACPYPE, few changed regarded default
> parameters.
>
> Pay attention to these options:
>
> -a ATOM_TYPE, --atom_type=ATOM_TYPE
> atom type, can be gaff or amber (AMBER14SB),
> default
> is gaff
>
> -z, --gmx4 write RB dihedrals old GMX 4.0 (default is NOT, for
> GMX >=4.5)
>
> (whatever option you take whether using -z or not, GMX will pick the right
> function).
>
> And be aware that you ligand may not have the right charge distribution
> profile, so it may run fine alone, but when in the ligand pocket site of
> the protein, high repulsive forces may show up.
>
>
>
> ================================================================================================
> | ACPYPE: AnteChamber PYthon Parser interfacE v. 2015-11-02 10:03:43Z Rev:
> 8810 (c) 2016 AWSdS |
>
> ================================================================================================
> Usage:
> acpype -i _file_ [-c _string_] [-n _int_] [-m _int_] [-a _string_] [-f]
> etc. or
> acpype -p _prmtop_ -x _inpcrd_ [-d]
>
> output: assuming 'root' is the basename of either the top input file,
> the 3-letter residue name or user defined (-b option)
> root_bcc_gaff.mol2: final mol2 file with 'bcc' charges and 'gaff' atom
> type
> root_AC.inpcrd : coord file for AMBER
> root_AC.prmtop : topology and parameter file for AMBER
> root_AC.lib : residue library file for AMBER
> root_AC.frcmod : modified force field parameters
> root_GMX.gro : coord file for GROMACS
> root_GMX.top : topology file for GROMACS
> root_GMX.itp : molecule unit topology and parameter file for
> GROMACS
> root_GMX_OPLS.itp : OPLS/AA mol unit topol & par file for GROMACS
> (experimental!)
> em.mdp, md.mdp : run parameters file for GROMACS
> root_NEW.pdb : final pdb file generated by ACPYPE
> root_CNS.top : topology file for CNS/XPLOR
> root_CNS.par : parameter file for CNS/XPLOR
> root_CNS.inp : run parameters file for CNS/XPLOR
> root_CHARMM.rtf : topology file for CHARMM
> root_CHARMM.prm : parameter file for CHARMM
> root_CHARMM.inp : run parameters file for CHARMM
>
> Options:
> -h, --help show this help message and exit
> -i INPUT, --input=INPUT
> input file name with either extension '.pdb',
> '.mdl'
> or '.mol2' (mandatory if -p and -x not set)
> -b BASENAME, --basename=BASENAME
> a basename for the project (folder and output
> files)
> -x INPCRD, --inpcrd=INPCRD
> amber inpcrd file name (always used with -p)
> -p PRMTOP, --prmtop=PRMTOP
> amber prmtop file name (always used with -x)
> -c CHARGE_METHOD, --charge_method=CHARGE_METHOD
> charge method: gas, bcc (default), user (user's
> charges in mol2 file)
> -n NET_CHARGE, --net_charge=NET_CHARGE
> net molecular charge (int), for gas default is 0
> -m MULTIPLICITY, --multiplicity=MULTIPLICITY
> multiplicity (2S+1), default is 1
> -a ATOM_TYPE, --atom_type=ATOM_TYPE
> atom type, can be gaff or amber (AMBER14SB),
> default
> is gaff
> -q QPROG, --qprog=QPROG
> am1-bcc flag, sqm (default), divcon, mopac
> -k KEYWORD, --keyword=KEYWORD
> mopac or sqm keyword, inside quotes
> -f, --force force topologies recalculation anew
> -d, --debug for debugging purposes, keep any temporary file
> created
> -o OUTTOP, --outtop=OUTTOP
> output topologies: all (default), gmx, cns or
> charmm
> -z, --gmx4 write RB dihedrals old GMX 4.0
> -t, --cnstop write CNS topology with allhdg-like parameters
> (experimental)
> -e ENGINE, --engine=ENGINE
> engine: tleap (default) or sleap (not fully
> matured)
> -s MAX_TIME, --max_time=MAX_TIME
> max time (in sec) tolerance for sqm/mopac, default
> is
> 10 hours
> -y, --ipython start iPython interpreter
> -w, --verboseless print nothing
> -g, --disambiguate disambiguate lower and uppercase atomtypes in GMX
> top
> file
> -u, --direct for 'amb2gmx' mode, does a direct conversion, for
> any
> solvent
> -l, --sorted sort atoms for GMX ordering
> -j, --chiral create improper dihedral parameters for chiral
> atoms
> in CNS
>
>
> On 13 January 2016 at 13:42, tarak karmakar <tarak20489.gmail.com> wrote:
>
> > Dear All,
> > I have a confusion related to two dihedral parameters that are present in
> > ffbonded.itp file,
> > X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
> > X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
> >
> > the similar dihedral parameters from parm99SBgaff.dat (GAFF) file,
> > X -oh-p5-X 3 1.600 0.000 3.000
> > X -os-p5-X 3 2.400 0.000 2.000
> >
> > As you see, there is a mismatch between the periodicity (last column) of
> > the similar dihedral angle from AMBER99SB and gaff databases.
> >
> > Would anybody like to comment on this?
> > I just read an earlier discussion in the following link,
> > http://dev-archive.ambermd.org/200506/0023.html
> > But, my problem is little more than the above.
> >
> > I am currently simulating a protonated pyrophosphate ligand molecule in a
> > protein. During the heating step in NVT ensemble (within 150-200 ps, 200
> K
> > temp), the atoms present in the phosphate groups (P,O and H) are showing
> > bizarre bonds and angles. I tried with the higher force constants (10
> times
> > than the existing one) for the above mentioned dihedral angles, and then
> > the molecule was behaving fine.
> >
> > Has anybody experienced this type of issue?
> > I appreciate any suggestions.
> >
> > Regards,
> > Tarak
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Tarak
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Received on Fri Jan 15 2016 - 09:00:03 PST
