[Dock-fans] amber parameter

Scott Brozell sbrozell at rci.rutgers.edu
Tue Sep 24 02:50:07 PDT 2013


Hi,

On Tue, Sep 24, 2013 at 11:27:46AM +0800, 963491781 wrote:
> I have to generate parameter for NADH.

Ok.
In general, this is a more difficult task than using available parameters at
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
and following the relatively simple recipe at
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/custom.html

> For this I have got mol2 file of NADH from LDHA pdb file(1I10).
>  Using antechamber I have generated lig_charged.ante.mol2 file and then use parmchk to generate frcmod file.
>
>  remark goes here
> MASS
>
> BOND
>
> ANGLE
> oh-ce-n2   74.360     122.080   same as n2-c2-oh
>
> DIHE
> ca-ca-ce-oh   1    6.650       180.000           2.000      same as X -c2-ce-X
> ca-ca-ce-n2   1    6.650       180.000           2.000      same as X -c2-ce-X
> ca-ce-oh-ho   1    1.050       180.000           2.000      same as X -c2-oh-X
> ca-ce-n2-hn   1    4.150       180.000           2.000      same as X -c2-n2-X
> oh-ce-n2-hn   1    4.150       180.000           2.000      same as X -c2-n2-X
> n2-ce-oh-ho   1    1.050       180.000           2.000      same as X -c2-oh-X
>
> IMPROPER
> c3-ca-na-cc         1.1          180.0         2.0          Using default value
> h5-na-cc-nd         1.1          180.0         2.0          Using default value
> ca-ca-ca-nd         1.1          180.0         2.0          Using default value
> ca-nb-ca-nh         1.1          180.0         2.0          Using default value
> ca-hn-nh-hn         1.1          180.0         2.0          Using default value
> h5-nb-ca-nb         1.1          180.0         2.0          Using default value
> ca-na-ca-nb         1.1          180.0         2.0          Using default value
> ca-h4-ca-na         1.1          180.0         2.0          Using default value
> ca-ca-ca-ce         1.1          180.0         2.0          Using default value
> ca-n2-ce-oh         1.1          180.0         2.0          Using default value
> ca-ca-ca-ha         1.1          180.0         2.0          General improper torsional angle (2 general atom types)
>
> NONBON
>
> Then I used
> command prepare_amber.pl anchor_and_grow_scored.mol2 rec_noHe.pdb ,then the progress is wrong.so I check the amberize_receptor.out file
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: ce - oh
> Building angle parameters.
> Could not find angle parameter: ce - oh - ho
> Could not find angle parameter: ca - ce - oh
> Building proper torsion parameters.
> Building improper torsion parameters.
>  total 970 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
>  Quit
> Error: the output file, rec_noHe.prmtop, is not complete !
>  But in frcmod file their is no bond parameter and angle parameter is not integrated !
>
> So can anybody suggest me why missing parameters are not write in frcmod file and how to cope with it?
>
>  Sincerely,
> Sun Rong

It is likely that you used an antechamber from a recent Amber/AmberTools
installation.  However, you must use the antechamber that comes with Dock.
(Perhaps you need to undefine the AMBERHOME environment variable ?)

AmberTools13/dat/leap/parm/gaff.dat  line 386
ce-oh  395.9    1.3545       SOURCE4      23    0.0100

But dock6.6/parameters/leap/parm/gaff.dat
does not have ce-oh.

Rerun with 
dock6.6/bin/antechamber
dock6.6/bin/parmchk

scott



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