Dear Lachele,
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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> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed May 16 2012 - 23:00:02 PDT
