[AMBER] LEaP & improper parameters

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Wed, 05 Jun 2013 09:05:37 +0200

Dear All,

If one loads the same number of _improper_ dihedrals (FF parameters)
in LEaP using either the generic (i.e. improper defined with 'X'
letters) or the specific 'way' (no 'X' letter) LEaP does not
rigorously apply the same impropers...

I take an example:
- I first executed leaprc.ff99SB (so there are generic improper
dihedrals in parm99.dat) and saved the prmtop/prmcrd files for
ACE-TYR-NME: 10 impropers are generated.

- Then I loaded my own frcmod file with only specific impropers; see below:
CA-CA-C -OH 1.10000000e+00 180.0 2. taken from parm99.dat
CA-CA-CA-CT 1.10000000e+00 180.0 2. taken from parm99.dat
C -CT-N -H 1.10000000e+00 180.0 2. taken from parm99.dat
CT-N -C -O 1.05000000e+01 180.0 2. adapted from parm99.dat
CA-CA-CA-HA 1.10000000e+00 180.0 2. adapted from parm99.dat
C -CA-CA-HA 1.10000000e+00 180.0 2. adapted from parm99.dat
and saved the prmtop/prmcrd files for the same ACE-TYR-NME dipeptides

I compare the generated prmtop files:

  diff generic.top specific.top
230c230
< 39 48 -42 -45 18 54 42 -48 -51 18 
---
>     39    48   -42   -45    18    42    54   -48   -51    18
   -> One observes differences in the %FLAG DIHEDRALS_INC_HYDROGEN  
section of the prmtop file
Then, I used 'rdparm' to study these 10 impropers; saved the 'rdparm'  
output in two text files, that I compared:
  diff generic.txt specific.txt
63c63
< B   62:   1.100  3.14  2.0    :1.CZ   :1.CD1  :1.CE1  :1.HE1  (19,15,17,18)
---
> B   62:   1.100  3.14  2.0    :1.CD1  :1.CZ   :1.CE1  :1.HE1  (15,19,17,18)
A single CA-CA-CA-HA improper is different; however, there are 4  
CA-CA-CA-HA impropers in the Tyrosine residue; this means 3 are  
applied using an homogeneous way, and for one the two first atoms are  
inverted.
Obviously I understand that the impact on the energy value is  
negligible, but this is quite painful when one tries to generate  
identical prmtop files:
Any idea where/how to correct that in the LEaP source code?
thank you
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 05 2013 - 00:30:03 PDT
Custom Search