anomalous behaviour of ASPP and GLUP during MD run

From: Andreini Matteo (mandreini_at_sienabiotech.it)
Date: Thu Feb 25 2010 - 02:31:45 CST

Hi all,
I found a strange behaviour of the protonated patched residues of ASP and GLUP. I patched two residues (ASP and GLU) in the protonated form ASPP and GLUPP and at the end of the psf generation all seems to work fine and the two residues are correctly patched. When I start the simulation the hydrogen added to the carboxy sidechain collapse toward the other oxygen of the carboxylic sistem:

Stating point
! HB1 OD1
! | //
! -CB--CG
! | \
! HB2 OD2-HD2

After few steps:
! HB1 OD1
! | //
! -CB--CG HD2
! | \ |
! HB2 OD2

Giving a look at the atom types of patched aminoacids all semms ok.

    4301 Q 305 ASP CB CT2 -0.210000 12.0110 0
    4302 Q 305 ASP HB1 HA 0.090000 1.0080 0
    4303 Q 305 ASP HB2 HA 0.090000 1.0080 0
    4304 Q 305 ASP CG CD 0.750000 12.0110 0 <--
    4305 Q 305 ASP OD1 OB -0.550000 15.9990 0 <--
    4306 Q 305 ASP OD2 OH1 -0.610000 15.9990 0 <--
    4307 Q 305 ASP HD2 H 0.440000 1.0080 0 <--
    4308 Q 305 ASP N NH1 -0.470000 14.0070 0
    4309 Q 305 ASP HN H 0.310000 1.0080 0
    4310 Q 305 ASP CA CT1 0.070000 12.0110 0
    4311 Q 305 ASP HA HB 0.090000 1.0080 0
    4312 Q 305 ASP C C 0.510000 12.0110 0
    4313 Q 305 ASP O O -0.510000 15.9990 0

Thanks
Matteo Andreini

________________________________

 [cid:logosienabiotech_trasparente_piccolo489c.gif] <http://www.sienabiotech.it/>

Matteo Andreini
Drug Design

Siena Biotech S.p.A.
Strada del Petriccio e Belriguardo, 35
53100 Siena - ITALY
Tel :(+39) 0577 381 415
Fax :(+39) 0577 381 410
mandreini_at_sienabiotech.it
www.sienabiotech.it<http://www.sienabiotech.it/>

________________________________
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.


logosienabiotech_trasparente_piccolo489c.gif

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:46 CST