AMBER Archive (2003)

Subject: parm99

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Tue May 20 2003 - 07:55:17 CDT

Dear all,

First I would like to thank all the persons who did answer my earlier
question.
I understand now that it was a stupid question but I was tired after
looking listings all the day.

I have a new question that I hope is less stupid.
There is still something I do not understand with parm99. In parm99.dat,
there are lots of new parameters,
including some new parameters for tyrosine concerning valence angles or
torsionnal angles.
Reading parm99.dat, I understand that these changes for tyrosine must be
done by changing the type of CZ atom
from C (in parm98) to CA (in parm99).
But looking at the topology file, it seems that Leap does not do this
modification....
Is there any problem with Leap, or is this just a little bug with no
incidence ?

Thank you in advance for your answer,
Fabien

Here is a part of a topology file made by Leap for a sequence {NGLY TYR
CGLY} :

leap script :
source leaprc.ff99
tmptyr = sequence { NGLY TYR CGLY}
savepdb tmptyr tmptyr.pdb
saveAmberParm tmptyr tmptyr.top tmptyr.crd
quit

topology file :
%FLAG ATOM_NAME
%FORMAT(20a4)
N H1 H2 H3 CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG CD1
HD1 CE1
HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA2 HA3 C O OXT

%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
N3 H H H CT HP HP C O N H CT H1 CT HC HC CA CA
HA CA
HA C OH HO CA HA CA HA C O N H CT H1 H1 C O2 O2 

--
__________________________________________________________________
Fabien Cailliez                         Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique      e-mail : cailliez_at_ibpc.fr
IBPC    13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________