[AMBER] Methyl groups

From: Imma Speciale <i.spec88.gmail.com>
Date: Fri, 21 Oct 2016 16:26:42 +0200

Dear all,

I have builded an olygosaccharide with GLYCAM-Web in order to open it with
Xleap, because this program generates a file pdb that Xleap usually open.
In my case, this is not true.

I have added in the file pdb the flag TER, to indicate the branching and I
have opened it in Xleap after loading *leaprc.GLYCAM_06h*, but the program
closes abnormally and in the terminal results the following message:


!FATAL ERROR----------------------------------------

!FATAL: In file [chirality.c], line 142

!FATAL: Message: Atom named CH3 from MEX did not match !




Thus I have loaded another library *leaprc.**GLYCAM_06j-1 *(the same
library used by GLYCAM-WEB to generate the oligosaccharide), but the result
is the same!!

Xleap doesn't recognize the flag MEX.

Does anyone know how to fix this?

Thank you
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Received on Fri Oct 21 2016 - 07:30:06 PDT
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