AMBER Archive (2008)

Subject: Re: AMBER: rdparm help

From: Alan (alanwilter_at_gmail.com)
Date: Mon Jun 23 2008 - 10:23:50 CDT

Many thanks Thomas!
However, I have more questions to this list.

Looking better the rdparm output, I noticed that every time I got 'E',
there's a line above it with the same atoms but with different parameters.

If I go and look and gaff.dat or parm99.dat I see dihedrals with the same
group of 4 atoms but with different parameters. I suspect that's why I have
this redundancy in prmtop/rdparm.out.

My question is: are those redundancy bad? It seems so to me. Which
parameters should be right? For gaff I can understand that it's a bit
"messy", but for parm**.dat? What if I simple delete those redundancy and
keep just the first set of parameters that appears?

My e-mail about parameters redundancy/duplication is some way related to the
questions did in http://amber.ch.ic.ac.uk/archive/200806/0289.html

Many thanks in advance.
Alan

On Fri, Jun 20, 2008 at 3:35 PM, Thomas Cheatham <tec3_at_utah.edu> wrote:

>
> > Playing with 'rdparm' -> printDihedrals, I got some lines starting with
> > letters 'E' or 'B' like:
> >
> > E 14: 2.500 3.14 2.0 :1_at_O :1_at_C :1_at_N1 :1_at_H
> (4,3,13,18)
> > B 92: 10.500 3.14 2.0 :1_at_CA :1_at_N1 :1_at_C :1_at_O
> (2,13,3,4)
> >
> > May anyone tell me what those letters mean?
>
> I = improper (no 1-4 electrostatic/vdw are calculated)
> E = excluded group (meaning 1-4's are not calculated)
> (this is usual when you have multiple terms for a given dihedral but
> only want to calculate the 1-4 interactions once)
> B = both E and I (meaning 1-4's are not calculated)
>
> -- tec3
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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