[AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ?

From: mish <smncbr.gmail.com>
Date: Tue, 26 Dec 2017 17:09:35 +0900

Dear all,

I wonder if it should be possible to read SCNB and SCEE entries from
frcmod file? I am using AmberTools16. Ligand is a modified GLYCAN and it
has dummy atom. I want to keep SCNB and SCEE to 1.0. The frcmod loaded to
tleap is in the following format:

-----ligand.frcmod--------
remark goes here
MASS
zz 0.000 0.000 ATTN, need revision
du 0.000 0.000 ATTN, need revision

BOND
Cg-zz 0.00 0.000 ATTN, need revision
zz-du 0.00 0.000 ATTN, need revision

ANGLE
C -Cg-zz 0.000 0.000 ATTN, need revision
Cg-zz-du 0.000 0.000 ATTN, need revision
Hc-Cg-zz 0.000 0.000 ATTN, need revision

DIHE
Ng-C -Cg-zz 1 0.000 0.000 0.000 SCEE=1.0,
 SCNB=1.0 ATTN, need revision
C -Cg-zz-du 1 0.000 0.000 0.000 SCEE=1.0,
 SCNB=1.0 ATTN, need revision
Hc-Cg-zz-du 1 0.000 0.000 0.000 SCEE=1.0,
 SCNB=1.0 ATTN, need revision
zz-Cg-C -O 1 0.000 0.000 0.000 SCEE=1.0,
 SCNB=1.0 ATTN, need revision

IMPROPER

NONBON
  zz 0.0000 0.0000 ATTN, need revision
  du 0.0000 0.0000 ATTN, need revision
----------

--leap.in--
source leaprc.GLYCAM_06j-1
loadAmberParams "./ligand.frcmod"
s = loadmol2 "./liagnd.mol2"
saveAmberParm s "ligand.parm7" "ligand.rst7"
quit 
---
I wonder if it is possible to have scnb=scee=1 set to those dihedrals
defined in frcmod file. Currently, leap set it those to default (last two
entries in my case are 1.2 and 2.0):
--parm7---
%FORMAT(5E16.8)
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.20000000E+00  1.20000000E+00  0.00000000E+00
0.00000000E+00
%FLAG SCNB_SCALE_FACTOR
%FORMAT(5E16.8)
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
1.00000000E+00
  1.00000000E+00  2.00000000E+00  2.00000000E+00  0.00000000E+00
0.00000000E+00
%FLAG SOLTY
----
Sincerely,
Mish
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Received on Tue Dec 26 2017 - 00:30:02 PST
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