Hi,
Thank you very much for response. Now all's clear. I've really
misunderstood you. By dihedral term I meant that term in Amber ff
represented by truncated Fourier series and not the total energy term
for 1-4 interactions. Therefore I've thought that you meant that there
was any other than Coulomb law dependence (multiplied by scaling
factor) on charge values for interactions of atoms in dihedrals.
Regards,
Kateryna
> Hi, sorry for the delay in the reply. I've cc'ed this response to the list, since I think it may be useful.
>
>
>>Frankly speaking, I'm confused because I've thought that dihedral term
>>is independent of charges values (at least in ff 94-99, I've not used
>>yet polarizable ff). It follows from AMBER ff equation http://amber.scripps.edu/eqn.txt
>>Well, may be I misunderstood something. Would you be so kind to
>>explain me what you meant.
>
> If you look in the AMBER9 manual:
> http://amber.ch.ic.ac.uk/doc9/amber9.pdf
>
> and search for the term SCEE. This is the 1-4 electrostatic scaling factor and the electrostatic interaction between 1-4 atoms is divided by this amount. One can gain
> explicit information about how the value is used in sander by grepping for scee in $AMBERHOME/src/sander/ene.f .Also, there is also a force field specific scaling factor
> for 1-4 VDW interactions as well; SCNB
>
> Hence, the dilhedral term is not an exclusive energy term for 1-4 interactions, and I'd agree with you that the equation at http://amber.scripps.edu/eqn.txt is misleading with
> respect to the dihedral term. For very old force fields, the the SCEE value used to be set to 2.0, but now (the default) is 1.2 for FF94. Be aware that there may be issues
> in using two force fields of different SCEE's (and SCNB's) within the same simulation, since there is no way to "tell" sander to treat each parameter set with its own
> SCEE value.
>
> Professor Thomas E. Cheatham speaks about this a bit in the following post:
> http://amber.ch.ic.ac.uk/archive/200505/0204.html
>
>
> Regards,
>
> Mark
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Received on Wed Apr 04 2007 - 06:07:42 PDT
