AMBER Archive (2003)

Subject: Re: bond command

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 14 2003 - 00:38:09 CST

On Wed, Feb 12, 2003, Craig A Bayse wrote:
>
> basically, i want to model cisplatin-dna complexes. i've modified the
> various dat/leap/* files and the parameters load without error. for the
> current problem, i load the pdb file and do the following:
>
> bond cab.19.1 cab.5.16
> bond cab.19.1 cab.6.16
>
> saveamberparm cab cab.prmtop cab.inpcrd
>
> the error after 'Building proper torsion parameters'
> !FATAL ERROR-------------------------------------------------
> !FATAL: In file [unitio.c], ;line 1765
> !FATAL: Message 1-4: cannot add bond 136 568

What is the nature of the bonds you are adding (or of the atoms 136 and 568)?
Is there any chance that you are adding a bond that is already present?
Are you completing a "square", by adding a bond to two atoms that are already
separated by three bonds? If you leave out one or both of the "bond"
commands, does the error go away?

Basically, you need to try to figure out the details of the particular
part(s) of the system LEaP seems not to like.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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