AMBER Archive (2008)

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

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri Jun 13 2008 - 20:49:53 CDT

Dear Carlos,
 
Thank you for your comments.
 
I study the interaction between an DNA intercalator (organic aromatic molecule) with polymer and B-DNA (intercalated to a nicked DNA). However, similar results were obtained in both system, i.e. a negative vdw values and positive GB values. As the interaction for intercalation are know to be hydrophobic in nature. Could you mind to teach me if the intepretation that I made is reasonablefor intercalator-DNA binding ?
 
For the case of polymer, I got the force field parameters of the polymer and the intercalator with GAFF in Antechamber. Could you mind to let me know if it is correct and how to check if the radii are correct or not?
 
Best regards and many thanks,
 
Cat> Date: Fri, 13 Jun 2008 03:46:55 -0400> From: carlos.simmerling_at_gmail.com> To: amber_at_scripps.edu> Subject: Re: AMBER: MM-GBSA with very positive GB value> > 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> > ________________________________> > Discover the new Windows Vista Learn more!> -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to amber_at_scripps.edu> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)> to majordomo_at_scripps.edu
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