[AMBER] Regarding simulation of Organometallic compounds

From: dhaval patel <pateldhaval.in.gmail.com>
Date: Sat, 7 Jul 2018 16:41:52 +0530

Dear All,

I am trying to simulate a protein with series of organometallic compound.
For the same I followed MCPB.py program tutorial for HEME protein. But
since the compound I am using is Ferrocene which has two separate cpc ring
with sandwiched Fe ion antechamber gives the following error.

This molecule may have more than one unit.
       antechamber can only handle one unit. If the input is a single unit
       then the connectivity is wrong and the geometry may be bad.
       Please convert your molecule to a mol2 file via:
       antechamber -j 5 -at sybyl -dr no
       And then check your molecule with a visualization program;
       manually add missing bonds or delete unwanted bonds as

I was wondering that the same issue is with FAJYAR01 example as given in
MCPB.py paper SI. How did they solved the issue?

Meanwhile if some one can provide or help me in getting ff parameters for

Any help will be appreciated.

Sincerely yours,
Dhaval Patel | PhD
The M. S. University of Baroda, Vadodara.
Lab: Biophysics & Structural Biology,
Indian Institute of Advanced Research,
Gujarat, INDIA. +91 9925450504
pateldhaval.in.gmail.com; dhaval.iiar.res.in
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Received on Sat Jul 07 2018 - 04:30:02 PDT
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