Date: Sat, 25 Apr 2020 20:39:45 +0530
Dear all,
I have done a simulation on an aromatic ligand which must remain planar. I
optimized the structure in Gaussian, done docking on the ligand, calculated
ESP charges for selected conformers in Gaussian again. My ligand has a +2
charge. Then I have done the RESP fitting using antechamber and generated
the frcmod file.
antechamber -fi gout -i ligand.log -fo prepi -o ligand.prepi -c resp
parmchk2 -i ligand.prepi -o ligand.frcmod -f prepi.
Then I performed restrained minimization, heating and density equilibration
and unrestrained equilibration and 500ns production. My ligand strangely
loses the planarity by the equilibration stage and shows a really distorted
structure which is unacceptable. I have used the gaff ff and Tip3p waterbox
in the simulation. My frcmod file looks like the following:
DIHE
ca-ca-cc-cc 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
ca-ca-cc-cf 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
ca-cc-cf-ha 4 16.000 180.000 2.000 same as X
-cc-cd-X , penalty score=136.0
ca-cc-cf-cf 4 16.000 180.000 2.000 same as X
-cc-cd-X , penalty score=136.0
cc-cc-cf-ha 4 16.000 180.000 2.000 same as X
-cc-cd-X , penalty score=136.0
cc-cc-cf-cf 4 16.000 180.000 2.000 same as X
-cc-cd-X , penalty score=136.0
IMPROPER
c3-ca-na-cc 1.1 180.0 2.0 Using the
default value
ca-ca-ca-na 1.1 180.0 2.0 Using the
default value
ca-ca-ca-cc 1.1 180.0 2.0 Using the
default value
ca-ca-ca-ha 1.1 180.0 2.0 Using general
improper torsional angle X- X-ca-ha, penalty score= 6.0)
cc-h4-cc-na 1.1 180.0 2.0 Using the
default value
ca-cc-cc-cf 1.1 180.0 2.0 Using the
default value
cc-cf-cf-ha 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 46.8 (use general term))
c3-ca-na-cd 1.1 180.0 2.0 Using the
default value
cc-h4-cd-na 1.1 180.0 2.0 Using the
default value
cc-cd-cc-ha 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 38.9 (use general term))
Could someone suggest what might have went wrong and how to solve this
issue. I am attaching the image of my distorted ligand here.
My two major doubts are
1. Is the frcmod file wrong?
2. should I include the -nc flag in the resp fitting since my ligand has
a +2 charge?
Thanks in advance
-- Jenny R.S Sir Syed College, Taliparamba, Kannur, Kerala
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(image/png attachment: nnnnn.PNG)
