[AMBER] is it possible to improve amino acids dihedral angles using Amber?

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Tue, 08 Jun 2010 16:21:58 +0400

Dear Amber users,
I did the anaylsis of representative structures (got by ptraj) from protein Amber molecular dynamics trajectory with TIP3P explicit solvent and I've made several thousands steps of conjugated gradient and steepest descent minimizations in sander for 248 amino acid protein. I've used both explicit, implicit solvents and in vacuo minimization (about 12 protein conformations in each case). Generally in all cases all parameters were optimized well and were in good ranges for example in MolProbity, except...Ramachandran favorable regions and disallowed. Generally I was a bit surprised by this as far as dihedral angles I was supposed to be always optimized using long enough molecular mechanics methods. I just wonder how can I optimize them - by just maybe increasing again the number of cycles, changing CG and SD ratio or I need to use something else.

Sincerely yours,

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Received on Tue Jun 08 2010 - 05:30:07 PDT
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