You may create two or more atom types to discriminate the two different bond
angles.
Good luck
Junmei
Sent from my Huawei Mobile
-------- Original Message --------
Subject: [AMBER] PF6- octahedral geometry change during equilibration!!
From: Sanaa ALAbbad
To: AMBER Mailing List
CC:
Dear Ambers,
I have an issue with PF6- conformational structure. During the
equilibration step, the octahedral geometry destroyed to square pyramidal.
I first used the frcmod generated by AMBER
remark goes here
MASS
p5 30.970 1.538
f 19.000 0.320
BOND
p5-f 248.60 1.646
ANGLE
f -p5-f 44.040 90.000
DIHE
IMPROPER
NONBON
f 1.7460 0.0610
p5 2.0940 0.2000
and then I included the 180 angle and use the parameters used by Phys.
Chem. Chem. Phys., 2003,5, 3481-3488
that destroyed the structure even more
remark goes here
MASS
p5 30.970 1.538
f 19.000 0.320
BOND
p5-f 260.30 1.646
ANGLE
f -p5-f 194.100 90.000
f -P5-f 194.100 180.00
DIHE
IMPROPER
NONBON
f 1.7460 0.0610
p5 2.0940 0.2000
Yet no luck!!
I tried to use PARAMFIT but it defined only one angle of 90.
Could any one help me with this regard?
Thanks in advance.
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Received on Thu Nov 30 2017 - 18:30:03 PST
