Hu Zhongqiao wrote:
Thanks a lot, Mark Abraham and David,
I thought the atom charge of an ALA molecule was same as those in ALA
residue of a protein molecules. That's wrong.
Now I can use pdb2gmx -ter to set zwitterion-type ALA.
About ffG43a1, I want to ask a question which is a little ambiguous to
me.
According to what someone said in mailing list, the force fields of
D-amino acids and L-amino acids are same. One just needs set different
coordinates for them and use the same force field. In fact I am not sure
for this. But when I used the ALA residue name for both D- and L-
alanine .pdb files and do energy minimization, the D-alanine quickly
flip to L-alanine. So it seems I am missing something.
I check ffG43a1.rtp and only difference for ALA and DALA is
ALA
[ impropers ]
; ai aj ak al gromos type
CA N C CB gi_2
DALA
[ impropers ]
; ai aj ak al gromos type
CA C N CB gi_2
I don't know what is the real difference for the order CA-N-C-CB and
CA-C-N-CB. It is said that the improper angle is the angle between i, j,
k and j, k, l. So I think the order CA-N-C-CB and CA-C-N-CB makes no
difference, right? I hope I am not right so that I can change something
to make sure that D-alanine does not flip to L-alanine. Anyone can give
a somehow detailed clarification for this,
Zhongqiao
look up the gi_2 definition, and make a dgi_2 definition with the angle
negative. ffGxxxbon.itp
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
