AMBER Archive (2003)

Subject: RE: parm99

From: Bayly, Christopher (christopher_bayly_at_merck.com)
Date: Thu May 22 2003 - 08:36:18 CDT

Dave,

Junmei's proposal to change the atom type of C-OH in tyrosine from C to CA
is excellent for another reason: it must be changed in order to get correct
torsional behaviour in any benzoyl small molecule fragment(benzoyl is
phenyl-C=O) e.g. benzamides.

benzoyl fragments crop up very frequently in e.g. aspartyl protease
inhibitors and they have a very soft X-CA-C-X torsion; in most Xray
structures they are significantly non-planar. Because of tyrosine, the
parm94 torsion X-CA-C-X is very tightly planar (i.e. high barrier) by
analogy with benzene. If tyrosine C-OH is changed to CA-OH, both tyrosine
and benzoyl torsions can be parameterized to behave correctly with parm94.

Christopher Bayly

-----Original Message-----
From: Junmei Wang [mailto:jwang_at_tbc.com]
Sent: Wednesday, May 21, 2003 2:30 PM
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: parm99

Hi, Dave,
I have tested the antechamber code for 40 molecules used by Christ Bayly.
The new scheme works fine. The programs are much faster and the algorithms
are more clear. I will load the revised code to chagall.scripps.edu after I
finish testing another 80 molecules. I will also add some force field
parameters to gaff.dat and then revise the papers ... Hopefully, I can
finish all the staff in two weeks.

As to the atom type of C-OH in tyrosine, I prefer to change its atom type
from C to CA in parm94 and parm96 based on the following reasons:
(1) first of all, we do not need make large change on parm94.dat and
parm96.dat (only change one bond length from 1.409 to 1.4)
(2) consistent with ff02 and parm99
(3) consistent with the atom type definition

The following is the parameters involved in parm94

C -CA 469.0 1.409 JCC,7,(1986),230; TYR
CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
C -OH 450.0 1.364 JCC,7,(1986),230; TYR
CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA
tyr
CA-C -OH 70.0 120.00 AA tyr
C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
CA-CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
X -C -CA-X 4 14.50 180.0 2. intrpol.bsd.on
C6H6
X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on
C6H6
X -C -OH-X 2 1.80 180.0 2.
JCC,7,(1986),230

If we change C to CA, only bond length CA-C(CA) changed slightly from 1.409
to 1.400. Other parameters are exactly same.

If we want to do this, we need add three additional parameters

CA-OH 450.0 1.364 JCC,7,(1986),230; TYR
CA-CA-OH 70.0 120.00 AA tyr
X -CA-OH-X 2 1.80 180.0 2.
JCC,7,(1986),230

Best

Junmei

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             "David A. Case"
             <case_at_scripps.edu
> To
                                       cailliez <Fabien.Cailliez_at_ibpc.fr>
             05/20/2003 05:37 cc
             PM amber_at_heimdal.compchem.ucsf.edu,
                                       jwang_at_tbc.com
                                                                   Subject
             Please respond to Re: parm99
             amber_at_heimdal.com
              pchem.ucsf.edu
                                                                           
                                                                           
                                                                           
                                                                           

On Tue, May 20, 2003, cailliez wrote:

> 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).

This looks like a bug to me: there doesn't seem to be any easy way to
use the parm99 tyrosine parameters for non-polarizable simulations, since
all_amino94.in still has the old atom types. [The polarizable libraries,
like all_amino02.in and all_amino02EP.in *do* have this change.]

Junmei: do you have a recommended solution for this?

The only workaround I see is to manually modify the TYR unit to change the
atom type of CZ, before loading in your pdb file.

Thanks for the report ... we'll try to figure out the best fix (so as not
to break older simulations that use ff94). This change is probably pretty
minor, but definitely looks to me like it is wrong.

..regards...dac 

--

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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