On Mon, Oct 21, 2013 at 4:58 AM, Bajarang Kumbhar <kumbharbajarang.gmail.com
> wrote:
> Dear Sir
> i am trying to do simulation of protein having heme, trimethylysine
> and SO4 group. So i use the prepin and frcmod file for heme and
> trimethyllysine from parameter database WHEREAS for SO4 group the files are
> generated using RED server. But after loading the files in xLeap it gives
> error such as loadamberprep hem.prepin
> *using Parm.ff99SB*
> Loading Prep file: ./hem.prepin
> > loadamberparams hem.frcmod
> Loading parameters: ./hem.frcmod
> Reading force field modification type file (frcmod)
> > loadamberprep Me3.prepin
> Loading Prep file: ./Me3.prepin
> > loadamberparams Me3.frcmod
> Loading parameters: ./Me3.frcmod
> > SO4=loadmol2 SO4.mol2
> Loading Mol2 file: ./SO4.mol2
> Reading MOLECULE named SO4
> > loadamberparams SO4.frcmod
> Loading parameters: ./SO4.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> FRCMOD file generated by R.E.D. Python version Octobre-3-2013 -
> q4md-forcefieldtools.org
> > protein=loadpdb protein.pdb
> Loading PDB file: ./protein.pdb
> One sided connection. Residue: missing connect1 atom.
> One sided connection. Residue: TP3 missing connect0 atom.
> total atoms in file: 1014
> Leap added 1119 missing atoms according to residue templates:
> 1119 H / lone pairs
> > edit protein
> > saveamberparm protein protein.prmtop protein.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
> -- ignoring the warning.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: SH - CY
> Could not find bond parameter for: SH - CY
> Could not find bond parameter for: NA - FE
> Could not find bond parameter for: S - FE
> Could not find bond parameter for: S - O
> Could not find bond parameter for: S - O
> Could not find bond parameter for: S - O
> Could not find bond parameter for: S - O
> Building angle parameters.
> Could not find angle parameter: HS - SH - CY
> Could not find angle parameter: SH - CY - CB
> Could not find angle parameter: SH - CY - HC
> Could not find angle parameter: SH - CY - CX
> Could not find angle parameter: CT - SH - CY
> Could not find angle parameter: HS - SH - CY
> Could not find angle parameter: SH - CY - CB
> Could not find angle parameter: SH - CY - HC
> Could not find angle parameter: SH - CY - CX
> Could not find angle parameter: CT - SH - CY
> Could not find angle parameter: CW - NA - FE
> Could not find angle parameter: H - NA - FE
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - S
> Could not find angle parameter: CR - NA - FE
> Could not find angle parameter: CT - S - FE
> Could not find angle parameter: S - FE - NP
> Could not find angle parameter: S - FE - NO
> Could not find angle parameter: S - FE - NP
> Could not find angle parameter: S - FE - NO
> Could not find angle parameter: CT - S - FE
> Could not find angle parameter: O - S - O
> Could not find angle parameter: O - S - O
> Could not find angle parameter: O - S - O
> Could not find angle parameter: O - S - O
> Could not find angle parameter: O - S - O
> Could not find angle parameter: O
> Building proper torsion parameters.
> ** No torsion terms for HS-SH-CY-CB
> ** No torsion terms for HS-SH-CY-HC
> ** No torsion terms for HS-SH-CY-CX
> ** No torsion terms for CT-SH-CY-CB
> ** No torsion terms for CT-SH-CY-HC
> ** No torsion terms for CT-SH-CY-CX
> ** No torsion terms for HS-SH-CY-CB
> ** No torsion terms for HS-SH-CY-HC
> ** No torsion terms for HS-SH-CY-CX
> ** No torsion terms for CT-SH-CY-CB
> ** No torsion terms for CT-SH-CY-HC
> ** No torsion terms for CT-SH-CY-CX
> ** No torsion terms for CW-NA-FE-NP
> ** No torsion terms for CW-NA-FE-NO
> ** No torsion terms for CW-NA-FE-NP
> ** No torsion terms for CW-NA-FE-NO
> ** No torsion terms for CW-NA-FE-S
> ** No torsion terms for H-NA-FE-NP
> ** No torsion terms for H-NA-FE-NO
> ** No torsion terms for H-NA-FE-NP
> ** No torsion terms for H-NA-FE-NO
> ** No torsion terms for H-NA-FE-S
> ** No torsion terms for NA-FE-S-CT
> ** No torsion terms for NA-FE-S-CT
> ** No torsion terms for CR-NA-FE-NP
> ** No torsion terms for CR-NA-FE-NO
> ** No torsion terms for CR-NA-FE-NP
> ** No torsion terms for CR-NA-FE-NO
> ** No torsion terms for CR-NA-FE-S
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> Building improper torsion parameters.
> old PREP-specified impropers:
> <M3L 72>: -M CA N H
> <M3L 72>: CA +M C O
> <HEM 105>: NA C1A C4A FE
> <HEM 105>: NB C1B C4B FE
> <HEM 105>: NC C1C C4C FE
> <HEM 105>: ND C1D C4D FE
> <HEM 105>: C1A C2A NA CHA
> <HEM 105>: C1B C2B NB CHB
> <HEM 105>: C1C C2C NC CHC
> <HEM 105>: C1D C2D ND CHD
> <HEM 105>: C2A C3A C1A CAA
> <HEM 105>: C2B C3B C1B CMB
> <HEM 105>: C2C C3C C1C CMC
> <HEM 105>: C2D C3D C1D CMD
> <HEM 105>: C3A C4A C2A CMA
> <HEM 105>: C3B C4B C2B CAB
> <HEM 105>: C3C C4C C2C CAC
> <HEM 105>: C3D C4D C2D CAD
> <HEM 105>: C4A NA C3A CHB
> <HEM 105>: C4B NB C3B CHC
> <HEM 105>: C4C NC C3C CHD
> <HEM 105>: C4D ND C3D CHA
> total 358 improper torsions applied
> 22 improper torsions in old prep form
> Building H-Bond parameters.
> Parameter file was not saved
>
> AFTER REMOVING THE SO4 GROUP FROM PDB IT GENERATE THE PRMTOP AND INPCRD
> FILES for PDB contain the HEME and trimethyllysine group using the
> parm.ff99SB force feild. PLEASE SUGGEST
>
You are missing a lot of parameters. You must provide these parameters in
the form of an frcmod file to leap so it knows what parameters to assign to
the different bonds. You can typically use "parmchk" on the library (i.e.,
mol2) files you have in order to generate at least a skeleton frcmod file
that will either find (hopefully) suitable parameters or provide
placeholders where you can insert your own.
If, on the other hand, you are drawing bonds in xleap (or otherwise
creating bonds inside LEaP itself) between the SO4 group and another
residue, you will either need to create a new residue library for the
original residue plus the SO4 group and pass that to parmchk in order to
get your frcmod file or use the list of missing parameters that leap prints
out to generate your own frcmod file.
The tutorials have numerous examples of creating library files (Tutorial
B4, for example) and frcmod files to help. You can also see the frcmod
file format described on
http://ambermd.org/formats.html
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 21 2013 - 05:00:02 PDT
