AMBER Archive (2005)

Subject: Re: AMBER: Minimized structure

From: Yam (yamwaikeat_at_yahoo.com)
Date: Thu Jul 28 2005 - 23:03:40 CDT

Dear Dr Thomas,

Hello.

I'm not too sure of that, maybe you can consult me by
looking at my output file?

Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of @type)...
Read in residue labels...
Read in the residue to atom pointer list...
Read in bond parameters RK and REQ...
Read in angle parameters TK and TEQ...
Read in dihedral parameters PK, PN and PHASE...
Read in SOLTY...
Read in L-J parameters CN1 and CN2...
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Read in info for angles w/ hydrogen...
Read in info for angles w/out hydrogen...
Read in info for dihedrals w/ hydrogen...
Read in info for dihedrals w/out hydrogen...
Read in excluded atom list...
Read in h-bond parameters: AG, BG, and HBCUT...
Read in atomic symbols (types)...
Read in tree information...
Read in the JOIN info...
Read in the IROTAT info...
Checking coordinates: rst

regards,
Yam

--- "Thomas E. Cheatham, III" <cheatham_at_chpc.utah.edu>
wrote:

>
> > Regards. I'm glad and thankful for your kind
> > explanation and I'm taking your advise to do a
> > "checkoverlap" to check for oo close contacts.
> > However, I'm facing some technical problem now as
> I do
> > not know how should I understand the output file.
>
> The output from checkoverlap comes right to the
> screen (stdout/stderr);
> you do not need to trajout an output trajectory (but
> you do need to read
> input coordinates with trajin). If there are any
> overlaps, ptraj will
> tell you (with output text starting with "OVERLAP").
> If there are none,
> then nothing will be reported.
>
>
>
>
>
>
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Wai Keat, Yam (Ms.)Molecular Simulation & Computation Group (MSC)Laboratory of Biocrystallography & Structural Bioinformatics (Makmal Biokristalografi & Bioinformatik Struktur),University Science Malaysia, Minden, 11800 Pulau Pinang,Malaysia.Tel: 604-6533888 ext. 2437

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