AMBER: doubts with a new aminoacid

From: Gustavo Pierdominici Sottile <gsottile.unq.edu.ar>
Date: Tue, 01 Feb 2005 17:28:52 -0300

Hi, I write because I have defined a new aminoacid and some problems appear
when using tleap.
One of them is that is I use the keyword desc, the following message appears
if the aminoacid is the new one:
No improper torsions
Contents:
But if it is any standard aminoacid, the message is this:
Improper torsions:
Contents:
 In none of them the list of improper torsions appears, but in standard ones
the message is different from the new one. I have already generate the file
to recognize this new aminoacid following the structure that have the other
ones. One part of this file is:

LOOP
 CG CD2
 CE2 CD2
IMPROPER
 -M CA N H
 CA +M C O
 CD1 CE2 NE1 HE1
 CE2 CH2 CZ2 OZ2
 CZ2 CZ3 CH2 NH2
 CH2 CE3 CZ3 HZ3
 CG NE1 CD1 HD1
 CD1 CD2 CG CB
DONE
STOP

 
Another doubt is that when writing check, the following warning appears, and
I donīt understand it
 WARNING: The unperturbed charge of the unit: -27.000000 is not zero.
 
Finally I would like to know if it is posible to change one specifyc van der
Walls interation. This is because I have defined a new atom type CS with the
same VDW parameters as CT (Ri 1.908 ei 0.1094). The VDW between CS and H1
(Rj 1.487 ej 0.086) is calculated obtaining VDW well depth Rij= Ri+ Rj and
eij= (ei*ej)**1/2. I need to change these parameters for this specifyc
interaction. Is it possible?
 
Thanking in advance
Gustavo
 


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Received on Tue Feb 01 2005 - 20:53:01 PST
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