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 AMBEr parameter database and for SO4 the files are
generated using RED server. But after loading the files in xLeap it gives
error such as
loadamberprep hem.prepin
Loading Prep file: ./hem.prepin
(no charges read on atoms lines in Heme residue ALL ATOM, Yves names,
Bayly-modified)
> loadamberparams hem.frcmod
Loading parameters: ./hem.frcmod
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for all-atom heme
Unknown keyword: N.B.: para in parameter file.
Unknown keyword: six-coo in parameter file.
Unknown keyword: Force fiel in parameter file.
Unknown keyword: Univers in parameter file.
Unknown keyword: in parameter file.
Unknown keyword: I modified in parameter file.
> loadamberprep Me3.prepin
Loading Prep file: ./Me3.prepin
> loadamberparams Me3.frcmod
Loading parameters: ./Me3.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> 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
Thanks
--
Dr. Kumbhar Bajarang Vasant
M.Sc. Ph.D.
Bioinformatics Group,
Department of Biochemistry,
Shivaji University Kolhapur- 416004
(M.S.), India.
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Received on Thu Oct 17 2013 - 23:00:04 PDT
