AMBER Archive (2005)

Subject: Re: AMBER: ambpdb TER problems

From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 30 2005 - 12:05:10 CST

On Wed, Dec 28, 2005, Sam wrote:
>
> Ok, this advice is very helpful and insightful, but based on the results
> I am not yet totally confident in the connectivity information of the new
> prmtop file.

Two suggestions:

1. use rdparm to investigate what bonds you have in the prmtop file.

2. don't use CONECT records in the pdb file to create crosslinks; better,
add them as "bond" commands in the leap input. This will also allow you
to use an output file from ambpdb (which does not include CONECT records)
as input back into LEaP.

[I'm always tempted to change LEaP to ingore CONECT records altogether,
because of problems like this: people may forget that they were there in some
initial pdb file, but not in later ones.]

....dac

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