Re: [AMBER] error message create parameters

From: David A Case <>
Date: Mon, 29 Jun 2020 14:27:40 -0400

On Mon, Jun 29, 2020, Renato Araujo wrote:

>I'm trying to build a protein-ligand system. The input is broken down here.

Can you break your big leap input into smaller pieces? In particular,
just try to load the ligand pdb and do the "saveamberparm lig ...."
part, and not the others.

The problem is that the pieces of the error message you included make it
hard to be sure which "saveamberparm" command is being executed when you
see the error message.

>!FATAL ERROR----------------------------------------
>!FATAL: In file [unitio.c], line 1810
>!FATAL: Message: 1-4: cannot add bond 1 2
>This may be caused by duplicate bond specifications;
>for example, explicit bond commands in addition to PDB conect records.

If this is happening in the ligand, double check your files. Is there a
bond between atoms 1 and 2? Can you see anything that might suggest
that somehow a request was made to make this bond twice?

>NOTE: I set up two other systems with different ligand with the same
>protein and did not present an error.

This strongly suggests that the problem is with the present ligand; but
beyond that, we don't have enough information to go further. But look
for differences between the ligands that "worked" and this one.


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Received on Mon Jun 29 2020 - 11:30:06 PDT
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