[AMBER] HEME parameters

From: Karan Mehra <kkm7r.virginia.edu>
Date: Thu, 9 Dec 2010 20:38:21 -0500

Hello Amber Experts,

I am trying to prepare amber input files for HORSE HEART CYTOCHROME
C<http://www.pdb.org/pdb/files/1HRC.pdb>.
I keep running into error messages that I believe deal with the
heme_all.inand frcmod
.heme files. I recently searched the previous messages in the mailing list
to look for solutions but I found no luck. Here is what I did:

-I downloaded the heme_all.in and heme.frcmod files from
http://www.pharmacy.manchester.ac.uk/bryce/amber.
-I edited these files according to the following suggestions found in a
previous email thread:

*(Issue #1) Add the following lines to the nonbonded (bottom) section
of the frcmod file:
  NO 1.8240 0.1700 OPLS
  NP 1.8240 0.1700 OPLS
  CX 1.9080 0.0860 Spellmeyer

 From looking at older parm*.dat files, these are the correct intended
parameters for these atom types.


(Issue #2) Move the partial charges from the bottom section of the
prep file to being the right-most column of the top section, e.g.:

    0 0 2
*
*
    Heme residue ALL ATOM, Yves names, Bayly-modified
*
*heme_all.db3
HEM INT 0
CORRECT OMIT DU BEG
   0.50000
   1 DUMM DU M 0 0 0 0.0000 0.0000
0.0000 0.0000
   2 DUMM DU M 1 0 0 1.4490 0.0000
0.0000 0.0000
   3 DUMM DU M 2 1 0 1.5220 111.1000
0.0000 0.0000
  19 FE FE M 16 14 12 2.1000 124.0000
180.0000 0.2500
  20 NA NP S 19 16 14 2.0800 98.0000
90.0000 -0.1800
... and so forth ...*

*- *I have attached the edited heme_all.in and frcmod.heme files

Here are the error messages which I am receiving:
[kkm7r.helium HEME]$ tleap
-I: Adding /itc/common/amber/10/amber10/dat/leap/prep to search path.
-I: Adding /itc/common/amber/10/amber10/dat/leap/lib to search path.
-I: Adding /itc/common/amber/10/amber10/dat/leap/parm to search path.
-I: Adding /itc/common/amber/10/amber10/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99SB
----- Source: /itc/common/amber/10/amber10/dat/leap/cmd/leaprc.ff99SB
----- Source of /itc/common/amber/10/amber10/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /itc/common/amber/10/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /itc/common/amber/10/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /itc/common/amber/10/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /itc/common/amber/10/amber10/dat/leap/lib/all_amino94.lib
Loading library: /itc/common/amber/10/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /itc/common/amber/10/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /itc/common/amber/10/amber10/dat/leap/lib/ions94.lib
Loading library: /itc/common/amber/10/amber10/dat/leap/lib/solvents.lib
> loadamberparams frcmod.hemall
Loading parameters: ./frcmod.hemall
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for all-atom heme
> loadamberprep heme_all.in
Loading Prep file: ./heme_all.in
Warning: per-line charges being overridden by CHARGE block in Heme
residue ALL ATOM, Yves names, Bayly-modified
> prot = loadpdb /home/kkm7r/pdb/cyt.pdb
Loading PDB file: /home/kkm7r/pdb/cyt.pdb
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C4D-ND-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C1D-ND-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CAC-CBC-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CAB-CBB-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C4B-NB-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C1B-NB-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-FE-NB-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-FE-ND-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
  total atoms in file: 869
  Leap added 880 missing atoms according to residue templates:
       880 H / lone pairs
> saveamberparm prot cyt.prmtop cyt.crd
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
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
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:
 <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 337 improper torsions applied
 20 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.

Can someone please help me with these error messages? I would really
appreciate it.

Best,
Karan Mehra
Chemical Engineering
University of Virginia 2012


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Received on Thu Dec 09 2010 - 18:00:02 PST
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