[AMBER] Problems in forcefield parameterization of Mercury

From: Muthukumaran Rajagopalan <kumaran.bicpu.edu.in>
Date: Tue, 16 Apr 2019 22:54:35 +0530

Dear AMBER users,

(i) I am trying to generate force field parameters for Mercury chloride connected via co-ordinate bond to amino acid. Antechamber recognises this coordinate bond as non-bonded. The command used is antechamber -i file.mol2 -fi mol2 -o min_sqm.mol2 -fo mol2 -c bcc -j5 -dr no. But parmchk is not able to define the bond and angle parameters correctly. how to rectify it?

(ii) Next, I tried to generate force field parameters by RESP method. The compound was optimised using Gaussian (Mp2; lanl2dz). The force constants are derived from frequency calculations. Can these frequencies used as force constants? Or any other alternatives to proceed?

Any suggestions and pointers regarding this would be very helpful.

Thanks in advance.

Muthukumaran Rajagopalan
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Received on Tue Apr 16 2019 - 10:30:02 PDT
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