Re: anomalous behaviour of ASPP and GLUP during MD run

From: La Fosca (magiofer_at_gmail.com)
Date: Thu Feb 25 2010 - 09:04:29 CST

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>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
>
> 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
>
>
>
> ------------------------------
>
> [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
> www.sienabiotech.it
>
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