I don't recommend changing the values for parameters we developed. If
you developed new ones, tleap will read them from the file if you add
them like that. In that case, you should use values appropriate to
how you developed the parameters.
I think it would be simplest to make a modified version of our
parameter file where you've added your new parameters. Then, just
load that into tleap. See the leaprc.GLYCAM_06h file in dat/leap/cmd
for a template.
On Thu, May 17, 2012 at 1:27 AM, Urszula Uciechowska
<urszula.uciechowska.chem.umu.se> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu May 17 2012 - 12:30:04 PDT
