AMBER Archive (2006)

Subject: RE: AMBER: problem with prep file

From: Junmei Wang (jwang_at_encysive.com)
Date: Mon May 15 2006 - 16:10:53 CDT

Hi Simon,
If there is no bond connectivity information in the input file,
antechamber tries to judge bond connection according to some simple
rules. It is understandable that the program may make mistakes when the
structure of the input molecule is very distorted (for example two
hydrogen atoms are separated less than a threshold, say 0.5 A, the
program assumes there is a bond formed between the two atoms). You may
avoid the possible flaw by using molecular formats such as mol2 and ac
(one needs to double check the bond field if it is produced by an input
file without bond connectivity).

Best regards

Junmei

Dear amber users,

I am getting a little frustrated trying to create a prep file for leap
for my substrate. I have converted a pdb file to prep file. When i check
the parameters using parmchk it creates a frcmod file with the unknown
bond lengths, angles, dihedrals etc generated. However when i change the
atom names in my prep file to match those of my pdb and repeat the
parmchk i get several values in the frcmod that require attention, for
example,

h1-h1 0.00 0.000 ATTN, need revision
ha-hn 0.00 0.000 ATTN, need revision
hc-hc 0.00 0.000 ATTN, need revision

This seems very strange indeed as there are no H-H bonds and the
connectivity in the prep file is unchanged.

Has anyone any ideas?

Regards

simon
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