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preeti Offline OP
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Dear All,

I posted my question in wrong forum, so here i am posting the same question aagin.

What is the parameter set to be used for GBSA for a system containing ATP in it?

The c30test/gbmv.inp recommends charmm19 parameter set, but it dosen't have ATP.

When I use charmm27 force field with stream file "toppar_all27_na_nad_ppi.str" i get total protein charge (+1) and upon adding ATP, protein+ATP charge becomes (-3). Adding Mg ions to neutralize ATP won't make any sense, until I use something like Lu(+3) ion.

What is the solution to the problem to make the total charge of the system neutral?

Thanks, preeti

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GBMV also works with the all atom charmm force fields, such that the protein-ATP complex you are studying should work well with CHARMM22. having a non-neutral total charge should not be a problem, but you may want to check the GB documentation as well as the original literature for more information.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

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