Urszula,
Concerning applying 1-4 scale factors, the GLYCAM FF uses different
values than AMBER. The GLYCAM FF uses also its own charge derivation
approach compared to AMBER.
We have used AMBER 1-4 scale factors following a highly consistent
charge derivation (Amber protocole) for a cyclodextrin based
glycopeptide and the results were more satisfactory than these
obtained with GLYCAM.
My feeling is that 1-4 scale factors depend on the charge derivation
procedure and dihedral FF parameters (which should be re-developed for
'some' sugar units).
Thus, you can use the 1-4 scale factors you wish if you rigorously
validate your approach. Thus, a good learning procedure for you would
be to run two jobs with the two types of scaling factors and study
what's going on...
regards, Francois
> Regarding applying 1-4 scale factors, In the manual for AMBER 12 I
> found that (pasted below)
>
> Usage: addDihedral <mask1> <mask2> <mask3> <mask4> <phi_k> <per> <phase>
> <scee> <scnb> [<type>]
> The dihedrals will be set with force constant phi_k, periodicity
> per, phase angle phase, 1-4 electrostatic
> scaling factor scee (this must be specified - the default Amber
> value is 1.2 and the default
> GLYCAM value is 1.0), the 1-4 van der Waals scaling factor scnb
> (this must be specified - the
> default Amber value is 2.0 and the default GLYCAM value is 1.0). The
> type is either "normal",
> "multiterm", or "improper". "multiterm" simply means that 1-4
> factors for that dihedral are
> not calculated, which should be true for all but the last term in a
> multiterm dihedral (so 1-4
> interactions are only counted once) and in some ring systems with at
> most 6 atoms, since that
> could also lead to double-counting specific 1-4 interactions.
>
> It is still not clear for me how to apply those factors, in the
> xleap/tleap? or its better to change it in the glycam_06g.dat file...
> Could anyone suggest me something?
> Urszula,
>
> check the LEaP manual, it should be explained there...
>
> regards, Francois
>
>
>> In the Glycam_06g.dat file I found quite long list of SCEE and SCNB
>> ... see below, it means that I should change the SCNB value for all
>> of them?
>> or should I add extra line somewhere?
>>
>>
>> O2-S -N -H 1 -0.10 0.0 6. SCEE=1.0
>> SCNB=1.0 N-Sulfates
>> O2-S -N -CG 1 0.11 0.0 -3. SCEE=1.0
>> SCNB=1.0 N-Sulfates
>> 1 0.0 0.0 -2.
>> SCEE=1.0 SCNB=1.0
>> 1 0.0 0.0 1.
>> SCEE=1.0 SCNB=1.0
>> S -N -CG-H1 1 0.02 0.0 3. SCEE=1.0
>> SCNB=1.0 N-Sulfates
>> S -N -CG-CG 1 0.0 0.0 -3. SCEE=1.0
>> SCNB=1.0 N-Sulfates
>> 1 -1.25 0.0 -2.
>> SCEE=1.0 SCNB=1.0
>> 1 -4.00 0.0 1.
>> SCEE=1.0 SCNB=1.0
>> CG-OS-CG-SM 1 0.67 0.0 -3. SCEE=1.0
>> SCNB=1.0 Thiol-linkages
>> 1 1.90 0.0 -2.
>> SCEE=1.0 SCNB=1.0
>> 1 1.14 0.0 1.
>> SCEE=1.0 SCNB=1.0
>> OS-CG-SM-CG 1 1.03 0.0 -3. SCEE=1.0
>> SCNB=1.0 (methoxymethyl)(methyl)sulfane
>> 1 1.44 0.0 -2.
>> SCEE=1.0 SCNB=1.0
>> 1 0.27 0.0 1.
>> SCEE=1.0 SCNB=1.0
>> H2-CG-SM-CG 1 0.0 0.0 1. SCEE=1.0
>> SCNB=1.0 (methoxymethyl)(methyl)sulfane
>> SM-CG-CG-H2 1 0.28 0.0 -3. SCEE=1.0
>> SCNB=1.0 (2,2-dimethoxyethyl)(methyl)sulfane
>> 1 0.04 0.0 -2.
>> SCEE=1.0 SCNB=1.0
>> 1 -0.21 0.0 1.
>> SCEE=1.0 SCNB=1.0
>> SM-CG-CG-OS 1 0.03 0.0 -3. SCEE=1.0
>> SCNB=1.0 (2-methoxyethyl)(methyl)sulfane
>> 1 0.18 0.0 -2.
>> SCEE=1.0 SCNB=1.0
>> 1 -1.03 0.0 1.
>> SCEE=1.0 SCNB=1.0
>> CG-SM-CG-H1 1 0.33 0.0 3. SCEE=1.0
>> SCNB=1.0 Dimethylsulfane
>> CG-CG-SM-CG 1 0.32 0.0 -3. SCEE=1.0
>> SCNB=1.0 Ethyl(methyl)sulfane
>>
>> /Urszula
>>
>> ________________________________________
>> Von: Lachele Foley (Lists) [lf.list.gmail.com]
>> Gesendet: Mittwoch, 16. Mai 2012 19:19
>> An: AMBER Mailing List
>> Betreff: Re: [AMBER] 1-4 scale factors
>>
>> You put them in the parameter file in the torsion section. See the
>> torsions section in the file $AMBERHOME/dat/leap/parm/GLYCAM_06h.dat
>> for examples. You just have to add the keyword/value pairs
>> "SCEE=value" and "SCNB=value" (no spaces between) in the comments
>> section of the appropriate lines.
>>
>>
>> On Wed, May 16, 2012 at 7:01 AM, Urszula Uciechowska
>> <urszula.uciechowska.chem.umu.se> wrote:
>>> Dear Amber users,
>>>
>>> I would like to somehow use the 1-4 scale factors, could someone
>>> tell me how to define it? should I do it in input file? or during
>>> the topology file preparations?
>>>
>>>
>>> | Note: 1-4 EEL scale factors were NOT found in the topology file.
>>> | Using default value of 1.2.
>>>
>>> | Note: 1-4 VDW scale factors were NOT found in the topology file.
>>> | Using default value of 2.0.
>>> | Duplicated 0 dihedrals
>>> | Duplicated 0 dihedrals
>>>
>>> /Urszula
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Received on Sat May 19 2012 - 00:00:04 PDT
