Hi Nitu,
To add to what Bill is written, there are in fact two problems with
these frcmod/prep files when using modern versions of AMBER/AmberTools:
(1) The atom types that were once defined in older force fields (NP NO
CX) are not present in the ff99 force fields.
(2) The partial charges in that prep file are not written in the
expected spot.
Here is what I've done to correct these issues with AMBER 11/AT 1.4:
(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 ...
Hope that helps,
Paul
P.S. If someone can see that I've done something terribly wrong here,
please let me know!
On Oct 14, 2010, at 11:07 AM, Nitu Bansal wrote:
> Dear all
>
> I have used hemeall files from
> http://www.pharmacy.manchester.ac.uk/bryce/amber
> these are i steps adopted. i am having difficulty in saving input
> copdinate
> and topology file.
>
> [root.localhost hemeall]# tleap -f leaprc.ff99SB
> -I: Adding /opt/amber10/dat/leap/prep to search path.
> -I: Adding /opt/amber10/dat/leap/lib to search path.
> -I: Adding /opt/amber10/dat/leap/parm to search path.
> -I: Adding /opt/amber10/dat/leap/cmd to search path.
> -f: Source leaprc.ff99SB.
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: /opt/amber10/dat/leap/cmd/leaprc.ff99SB
> Log file: ./leap.log
> Loading parameters: /opt/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: /opt/amber10/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /opt/amber10/dat/leap/lib/all_nucleic94.lib
> Loading library: /opt/amber10/dat/leap/lib/all_amino94.lib
> Loading library: /opt/amber10/dat/leap/lib/all_aminoct94.lib
> Loading library: /opt/amber10/dat/leap/lib/all_aminont94.lib
> Loading library: /opt/amber10/dat/leap/lib/ions94.lib
> Loading library: /opt/amber10/dat/leap/lib/solvents.lib
>> source leaprc.gaff
> ----- Source: /opt/amber10/dat/leap/cmd/leaprc.gaff
> ----- Source of /opt/amber10/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /opt/amber10/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic mol., add. info. at the end
> (June,
> 2003)
>> 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.prepin
> Loading Prep file: ./heme_all.prepin
> (no charges read on atoms lines in Heme residue ALL ATOM, Yves
> names,
> Bayly)modified
>> loadamberparams BHF.frcmod
> Loading parameters: ./BHF.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
>> loadamberprep BHF.prepin
> Loading Prep file: ./BHF.prepin
>> nitu= loadpdb cyp1a1.pdb
> Loading PDB file: ./cyp1a1.pdb
> total atoms in file: 4173
> Leap added 4140 missing atoms according to residue templates:
> 4140 H / lone pairs
>
>> saveamberparm nitu cyp.prmtop cyp.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> For atom: .R<HEM 513>.A<NA 2> Could not find type: NP
> For atom: .R<HEM 513>.A<NB 23> Could not find type: NO
> For atom: .R<HEM 513>.A<CBB 32> Could not find type: CX
> For atom: .R<HEM 513>.A<NC 39> Could not find type: NP
> For atom: .R<HEM 513>.A<CBC 48> Could not find type: CX
> For atom: .R<HEM 513>.A<ND 55> Could not find type: NO
> Parameter file was not saved.
>>
> please suggest me.
> i am very thankful for the previous responses.
>
> On Thu, Oct 14, 2010 at 5:07 PM, case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Thu, Oct 14, 2010, Nitu Bansal wrote:
>>> Reading force field modification type file (frcmod)
>>> Reading title:
>>> Force field modifcations for united atom heme, plus flexible water
>>> WARNING: expected Improper Torsion PK>0 (0.000000)
>>> Here is the Improper Torsion line in question:
>>> X CC CC X 0 0.000 180.000 2.000
>>> WARNING: expected Improper Torsion PK>0 (0.000000)
>>> Here is the Improper Torsion line in question:
>>> X CB NO X 0 0.000 180.000 2.000
>>> WARNING: expected Improper Torsion PK>0 (0.000000)
>>> Here is the Improper Torsion line in question:
>>> X CB NP X 0 0.000 180.000 2.000
>>> WARNING: expected Improper Torsion PK>0 (0.000000)
>>> Here is the Improper Torsion line in question:
>>> X CB CC X 0 0.000 180.000 2.000
>>
>> These are just informational messages...leap is asking if you
>> really want
>> an
>> improper torsion with zero force constant. In this case, you do.
>>
>> ...dac
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Nitu Bansal
> M.S Pharm III Sem
> Research Scholar
> Center for Pharmacoinformatics
> S.A.S Nagar NIPER Mohali (Chandigarh)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Oct 14 2010 - 12:00:04 PDT
