[AMBER] hydrogen bond charmm vs amber

From: newamber list <newamberlist.gmail.com>
Date: Thu, 15 Jan 2015 19:20:20 +0000

Hi All,

I have one DNA pdb with AMBER (ff10) atom names and same file with CHARMM36
atom names. Mainly difference are AMBER's C7, OP1, OP2 with their
respective names in CHARMM36 being C5M, O1P, O2P. Also there are many H
names differences.

I used these DNA pdbs to calculate number of Hydrogen bonds with cpptraj
natstruc but cpptraj complained about C5M atom in CHARMM case. After
correcting heavy atom names I got no error and found same number of H bonds.

I am getting correct results but just wondering as cpptraj does not
complain about expected H name (AMBER) as they are different in AMBER and
CHARMM. Is it due to somehow programme searches for generic *H* kind name?

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Received on Thu Jan 15 2015 - 11:30:03 PST
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