Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file

From: onetwo <>
Date: 27 Dec 2013 06:42:40 -0000

Dear Case,

Thanks for the reply.

I am attaching the leap.log file with the mail. I hope it will be helpful in suggesting the solution.

Thanks and Regards

On Thu, 26 Dec 2013 20:20:45 +0530 wrote

>On Thu, Dec 26, 2013, onetwo wrote:


> I have a protein with bound substrate which is phenyl ring with two

> chlorines attached to it. Chlorine have atom name: CLAM and CLAN


> FATAL: Atom .R.A does not have a type.

This is a very odd error; is it *exactly* what was printed? Usually there

would be numbers in addition to letters in such an error message. What

information is found before and after this message?

It's not obvious that this has anything to do with the chlorine atoms. Use

the "desc" command to examine your structure. Break the structure into

pieces, such as the ligand by itself, and see if things work.

If you can't figure it out, please post files for a small example that

illustrates the problem.



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Received on Thu Dec 26 2013 - 23:00:03 PST
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