amber-developers: Leap Improper Torsion Problems.

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 13 Oct 2005 10:28:02 -0700

Hi Everyone.

Has anybody managed to get improper torsions working as specified in an
frcmod file?

E.g. If I have NMA
     O
     |
CT-N-C-CT
   |
   H

There are two impropers I want to change:

CT-N-C-O & C-CT-N-H

These are defined in the parm99.dat file as:

X -X -C -O 10.5 180. 2.
C -CT-N -O 1.1 180. 2.

Now, if I modify these directly in the parm99.dat file all is good.
However,
I want to use the frcmod approach to modifying these.

So I specify the following frcmod file:

angles fitted
MASS

BOND
N-H 521.8079 1.0104
C-O 739.4008 1.2387
C-N 322.4874 1.3697
CT-C 227.9333 1.5105
N-CT 310.5384 1.4427

ANGL
C-N-H 39.4603 110.8903
H-N-CT 43.7170 109.3932
O-C-N 80.0535 121.7368
C-N-CT 71.0434 113.4190
CT-C-O 54.0136 123.3811
CT-C-N 58.8671 113.8363

DIHE
O-C-N-H 1 -15.3311 0.0 1.0
O-C-N-H 1 9.4589 180.0 2.0
CT-C-N-H 1 -0.0292 180.0 2.0
O-C-N-CT 1 3.6089 180.0 2.0
CT-C-N-CT 1 3.4041 180.0 2.0

IMPROPER
C -CT-N -H 0.2123 180. 2.
CT-N -C -O 14.5029 180. 2.

NONB

I then load tleap as follows:
/usr/local/amber9/exe/tleap

>source leaprc.ff03
>loadamberparams frcmod
>nma = loadpdb nma.pdb
>saveamberparm nma nma.prmtop nma.inpcrd

This creates the attached prmtop file. Now if I then look at this with
rdparm I find that the bonds angles and regular dihedrals have been
handled
correctly and the explicit specified ones in the frcmod file have
overidden
the ones in parm99.dat. However, the improper torsion parameters I
specified
in the frcmod file have been ignored and the ones from the parm99.dat file
are used:

Dihedral pk phase pn atoms
       1: -15.331 0.00 1.0 :1.O :1.C :2.N :2.H (6,5,7,8)
E 2: 9.459 3.14 2.0 :1.O :1.C :2.N :2.H (6,5,7,8)
...
B 22: 1.100 3.14 2.0 :1.C :2.CH3 :2.N :2.H (5,9,7,8)
...
B 25: 10.500 3.14 2.0 :1.CH3 :2.N :1.C :1.O (2,7,5,6)

So, it appears that while supposedly supported, specifying impropers in
the
frcmod file does not work. At least not to overide an existing parm.dat
parameter. This is very worrying since several of the frcmod files
provided
in $AMBERHOME/dat/leap/parm/ use this mechanism. E.g. frcmod.constph,
frcmod.ff03ua and frcmod.urea. Did the authors of these files ever
explicitly check that leap was doing what they though it was doing? And if
so how do you get it to work?

Note, this is not an issue with leap not reading the frcmod file correctly
but something much deeper in the internals. E.g. If you run xleap and load
the frcmod file into a parmset unit you can then edit that unit and see
the
impropers were read in. They are just not used when writing the prmtop
file.

xleap
>source leaprc.ff03
>frcmod = loadamberparams frcmod
>edit frcmod

Click on impropers and lo and behold they are there. They just don't
replace
anything from the parm99.dat file.

So, does anybody have a fix for this? Or know enough of the Leap source
code
to work out what is going on? I know I could modify the parm99.dat file to
get around this problem but this is not what we encourage users to do and
is
not really the best practice...

Comments?

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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Received on Wed Apr 05 2006 - 23:49:52 PDT
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