Dear Amber users,
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
Urszula Uciechowska, Ph.D.
Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
urszula.uciechowska.chem.umu.se
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Donnerstag, 17. Mai 2012 07:58
An: AMBER Mailing List
Betreff: Re: [AMBER] 1-4 scale factors
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 Thu May 17 2012 - 05:00:02 PDT
