AMBER Archive (2009)

Subject: [AMBER] IGB=7 vs IGB=5

From: guardiani_at_fi.infn.it
Date: Thu Jun 25 2009 - 06:20:15 CDT

Dear Amber experts,

I am currently performing REMD simulations of a glycopeptide in
implicit solvent. So far I have been using the IGB=7 Generalized
Born model, but I am wondering whether it could be more appropriate
to use IGB=5. In particular, answering to a different question to
the mailing list, Ross Walker suggested using IGB=5 since

"... the general consensus right now is that IGB=7 does not improve
over the previous GB results and can potentially make things worse."

I had chosen to use IGB=7 as I had read in

J. Chem. Theory Comput. 2007, 3, 156-169 and in
J. Phys. Chem. B 2007, 111, 1846-1857

that this particular implementation of the GB model is not affected
by a bias towards alpha-heical structures, as was the case of previous
implementations such as the OBC GB model.

I would like to know if there is any recent paper discussing the drawbacks
and limitations of the IGB=7 implementation of the GB model, and I would
also like to know why there is a general consensus on the fact that
IGB=7 may potentially make things worse as compared to previous
implementations
of the GB model.

I thank you very much for your help.

Best regards,

Carlo Guardiani

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> Hi Carlo,
>
>> Now my parametrization is as simple as that (I am using the bondi
>> radii because I want to try an implicit-solvent simulation with
>> igb=7, but of course I will also run the explicit-solvent one):
>
> Unless you have specific reasons for using IGB=7, say comparison to previous
> results, then I would suggest avoiding it and using IGB=5. I think the
> general consensus right now is that IGB=7 does not improve over the previous
> GB results and can potentially make things worse.
>
>> xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>>
>> set default PBradii bondi
>> source leaprc.glycam04
>> x = sequence { NVAL GLU ARG NLN GLY HIS CSER }
>> set x tail x.4.11
>> set 1GB head 1GB.1.1
>> y = sequence { x 1GB }
>> savepdb y y.pdb
>> saveamberparm y y.top y.crd
>> quit
>>
>>
>> Please let me know if this is what you meant. Which charges I will be
>> using with this parametrization ? Charges based on the Connolly surface
>> for the amino-acid residues and charges based on the CHELPG algorithm
>> for the sugar ?
>
> I would use RESP charges for everything. See: W.D. Cornell, P. Cieplak, C.I.
> Bayly & P.A. Kollman J. Am. Chem. Soc. 1993, 115, 9620-9631.
>
>> As for the 1-4 scaling factors, I performed my previous simulations
>> using the default values, e.g.
>>
>> SCNB = 2.0
>> SCEF = 1.2
>>
>> Are these values appropriate for a glycopeptide simulation ?
>> If I explicitly set these values in the .in input files of
>> my REMD simulation, will the apply to both the peptide and
>> the sugar parts ?
>
> There is a slight mismatch right now between the Glycam force field and the
> protein ones. The protein force fields all scale VDW by 2.0 and EEL by 1.2
> (I assume you meant SCEE above and not SCEF) which are the defaults. GLYCAM
> on the other hand does not do any scaling so would have SCNB = SCEE = 1.0.
> AMBER 10 does not support such mixing of different 1-4 scaling factors
> (AMBER 11 will support it) and thus at present you have to choose a
> compromise. I believe the current 'accepted practice' is just to use the
> defaults of 2.0 and 1.2 for everything when doing mixed protein /
> carbohydrate simulations.
>
> Good luck,
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
>
>
>
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