AMBER Archive (2008)

Subject: Re: AMBER: MM-GBSA with very positive GB value

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jun 13 2008 - 02:46:55 CDT

it might help if we know what the system is and where the
intrinsic radii come from. did you check the radii and make
sure they were all assigned correctly? leap is mostly good at
setting them for proteins/organic molecules, and if you have
something else it might not work as well. for non-standard
systems this needs to be checked carefully.

the large negative vdw does not indicate that it is hydrophobic,
just that there are strong vdw interactions. since there is no
dispersion interaction with the continuum water, the vdw term itself
is not a measure of the net vdw for transfer from gas phase
to water.

On Fri, Jun 13, 2008 at 3:05 AM, Catein Catherine
<askamber23_at_hotmail.com> wrote:
> Dear Sir/Madam,
>
> I did a MM-GBSA calculation for a short polymer, however, I found the
> following results very strange that GB is a positive value. I am trying to
> interpret the result as the polymer is hydrophobic (as indicated by the
> large negative VDW value) in nature, so it is not soluble in water. Thus, a
> positive (unfavor) solvation energy (GB) is obtained. Could anyone cold
> like comment on this if I have interpret that data correctly or I must have
> done something wrong in the calculation?
>
> Best regards and many thanks,
>
> Cat.
>
> ELE -6.3
> VDW -46.48
> INT -0.01
> GAS -52.8
> GBSUR -2.89
> GB 24.89
> GBSOL 22
> GBELE 18.59
> GBTOT -30.79
> TSTRA -12.92
> TSROT -10.76
> TSVIB 5.83
> TSTOT
>
> -17.85
>
>
> Thus,
>
> VDW+GBSUR
>
>
>
> -49.37
> ELE+GB 18.59
> GBTOT-TSTOT -12.94
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