AMBER Archive (2005)

Subject: Re: AMBER: TI - frcmod file

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Wed Jul 13 2005 - 16:18:08 CDT

Hi Ilyas,

I have done a test in order to find out about the effect of loading an
frcmod file on the torsional parameters:

I think it shows that the new parameters overwrite the old ones. Please
see below:

In xleap:

   after "source leaprc.gaff"
         saveamberparm GLY gly_99.top gly_99.crd
   after "source leaprc.gaff"
         loadamberparams test.frcmod
         saveamberparm GLY gly_test.top gly_test.crd

with test.frcmod:

DIHEDRAL
H1-CT-C -O 1 10.0110 0.00 -3.
H1-CT-C -O 1 0.0 0.00 1.

The dihedral force constant entries in the two top files look like this:

gly_99.top:
===========
%FLAG DIHEDRAL_FORCE_CONSTANT

%FORMAT(5E16.8)

   0.00000000E+00 8.00000000E-01 8.00000000E-02

gly_test.top:
=============
%FLAG DIHEDRAL_FORCE_CONSTANT

%FORMAT(5E16.8)

   0.00000000E+00 0.00000000E+00 1.00110000E+01

=> Loading the frcmod file has overwritten the torsions defined so far.
The first value comes from parm99.dat:
X -CT-N -X 6 0.00 0.0 2.

Oliver

---------------------
Ilyas Yildirim wrote:
> Hi Oliver,
>
> I am a little bit confused on one thing. Maybe someone can help me with
> this. Now, let's say we load the parameter files from parm99.dat first,
> and then the frcmod.03 file. First, the torsional parameters for CT-CT-C
> -N will be
>
> CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94
> CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94
>
> Then, after the second parameter load (frcmod.03), what will be the
> torsional parameters of CT-CT-C -N? I thought that the last column
> (above, it is -4 and 2) is defining if there are multiple torsional
> parameters for a particular torsion angle. So, if we wanted to change
> them, we should have used the following format: (at least that's what I
> have understood)
>
> CT-CT-C -N 1 XXXXX XXX -4.
> CT-CT-C -N 1 XXXXX XXX 2.
>
> But in frcmod.03 file, the torsional parameters for CT-CT-C -N are defined
> as following:
>
> CT-CT-C -N 1 0.0560 0.00 -3.
> CT-CT-C -N 1 0.0657 180.00 -2.
> CT-CT-C -N 1 0.7784 180.00 1.
>
> I am thinking that these extra three torsional parameters for CT-CT-C -N
> are going to be added on the CT-CT-C -N parameter list (because their PN
> number are different; -4,2,-3,-2,1). If I am wrong, please correct me. If
> it overwrites the parameter list, how does it do it? Just deletes the
> whole CT-CT-C -N torsional parameter list previously defined, and then
> adds the new parameter list?
>
> But for your case, I totally agree with you. The parameter is already
> defined in the force field for H0-CT-C -N. You dont have to change it
> to zero. But as I wrote above, I am confused on how the new parameter
> list are defined in AMBER when they are loaded. Hope someone can
> enlighten us with this.
>
> Best,
>
> On Tue, 12 Jul 2005, Oliver Hucke wrote:
>
>
>>Hi Ilyas,
>>
>>thanks for your detailed reply!
>>
>>So far I have one remark:
>>
>>
>>>I have checked out the ff03 parameters. The parameters for your system are
>>>defined in frcmod.ff03 and parm99.dat. Here are the parameters:
>>>- parm99.dat -
>>>CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94
>>>CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94
>>>---------------
>>>- frcmod.ff03 -
>>>CT-CT-C -N 1 0.0560 0.00 -3.
>>>CT-CT-C -N 1 0.0657 180.00 -2.
>>>CT-CT-C -N 1 0.7784 180.00 1.
>>>
>>>H0-CT-C -N 1 0.0110 0.00 -2.
>>>H0-CT-C -N 1 1.0607 180.00 1.
>>>---------------
>>>First the parm99.dat is loaded and then the frcmod.ff03 is loaded. As far
>>>as I see, there are 5 torsional parameter defined for CT-CT-C -N. That
>>>means that if you do a perturbation from CT-CT-C -N --> H0-CT-C -N, you
>>>need to defined 5 torsional parameter for H0-CT-C -N, too. (If I am wrong,
>>>please someone correct me)
>>
>>My understanding is that loading of the frcmod file with new parameters
>>for the CT-CT-C -N torsion will OVERWRITE the existing parameters. So,
>>after reading the frcmod file, 3 parameters are associated with this
>>torsion...
>>
>>This is also the reason why I do not understand that leap asks for the
>>redifinition of torsion parameters that are already loaded.
>>
>>Thanks again,
>>Oliver
>>
>>
>
> 

-- 
________________________________________________________________

Oliver Hucke, Dr.
Biomolecular Structure Center   Health Sciences Building - K418C
Dept. of Biochemistry           1959 NE Pacific St.
University of Washington        phone: (206) 685 7046
Box 357742                      fax  : (206) 685 7002
Seattle, WA 98195-7742          email: ohucke_at_u.washington.edu
________________________________________________________________

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu