RE: anomalous behaviour of ASPP and GLUP during MD run

From: Andreini Matteo (mandreini_at_sienabiotech.it)
Date: Thu Feb 25 2010 - 10:57:23 CST

Thanks Maria and Michel now it woks fine!

-------------------------------------------------------------
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 http://www.sienabiotech.it/
-----Original Message-----
From: Michel Espinoza-Fonseca [mailto:mef_at_ddt.biochem.umn.edu]
Sent: Thursday, February 25, 2010 5:52 PM
To: La Fosca
Cc: Andreini Matteo; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: anomalous behaviour of ASPP and GLUP during MD run

Matteo and Maria,

When applying a patch, you must regenerate the bond angles and dihedrals using the option "regenerate angles dihedrals" in psfgen. This should solve your problem.

Best,
Michel

On Feb 25, 2010, at 9:19 AM, "La Fosca" <magiofer_at_gmail.com<mailto:magiofer_at_gmail.com>> wrote:

Hello Matteo,
It happened to me too. The problem is that NAMD still considers your
residues as GLU and ASP, that is, charged residues without a proton. What I
did was to create two new residue types in the force field APP and GPP,
defining the topology with the proton included as if it was a "normal" part
of it (that is not using the patch), here my example

RESI GPP 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 OE1
ATOM HA HB 0.09 ! | | | //
GROUP ! HA-CA--CB--CG--CD
ATOM CB CT2 -0.18 ! | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.21 !
ATOM HG1 HA 0.09 ! HG1 OE1
ATOM HG2 HA 0.09 ! | //
ATOM CD CD 0.75 ! -CG--CD
ATOM OE1 OB -0.55 ! | \
ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2
ATOM HE2 H 0.44 !
GROUP
ATOM C C 0.51
ATOM O O -0.51
etc...

then in your pdb you have

ATOM 694 N GPP 44 -31.667 -2.386 8.302 1.00 0.00 PROT
ATOM 695 HN GPP 44 -30.979 -3.035 7.988 1.00 0.00 PROT
ATOM 696 CA GPP 44 -31.331 -1.688 9.519 1.00 0.00 PROT
ATOM 697 HA GPP 44 -32.223 -1.199 9.883 1.00 0.00 PROT
ATOM 698 CB GPP 44 -30.788 -2.682 10.582 1.00 0.00 PROT
ATOM 699 HB1 GPP 44 -31.625 -3.345 10.884 1.00 0.00 PROT
ATOM 700 HB2 GPP 44 -30.459 -2.091 11.461 1.00 0.00 PROT
ATOM 701 CG GPP 44 -29.602 -3.585 10.151 1.00 0.00 PROT
ATOM 702 HG1 GPP 44 -29.681 -3.772 9.059 1.00 0.00 PROT
ATOM 703 HG2 GPP 44 -29.681 -4.551 10.693 1.00 0.00 PROT
ATOM 704 CD GPP 44 -28.214 -2.996 10.432 1.00 0.00 PROT
ATOM 705 OE1 GPP 44 -28.116 -1.943 11.112 1.00 0.00 PROT
ATOM 706 OE2 GPP 44 -27.225 -3.632 9.982 1.00 0.00 PROT
ATOM 707 HE2 GPP 44 -26.873 -3.301 9.152 1.00 0.00 PROT
ATOM 708 C GPP 44 -30.323 -0.605 9.231 1.00 0.00 PROT
ATOM 709 O GPP 44 -30.043 0.231 10.089 1.00 0.00 PROT

then you shouldn't have any more problems. I think it is not the canonical
solution, but it works.

I hope that I helped.

greetings,
Maria

On Thu, Feb 25, 2010 at 2:24 PM, Andreini Matteo
<mandreini_at_sienabiotech.it<mailto:mandreini_at_sienabiotech.it>>wrote:

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 ß

   4305 Q 305 ASP OD1 OB -0.550000 15.9990
0 ß

   4306 Q 305 ASP OD2 OH1 -0.610000 15.9990
0 ß

   4307 Q 305 ASP HD2 H 0.440000 1.0080
0 ß

   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

------------------------------

[image: Siena Biotech S.p.a.] <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<mailto:mandreini_at_sienabiotech.it>
www.sienabiotech.it<http://www.sienabiotech.it>

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