AMBER Archive (2006)

Subject: Re: AMBER: erroneous placement of TER card

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 16 2006 - 10:20:32 CST

On Thu, Nov 16, 2006, Gregory Sandala wrote:
>
> | ERROR: Bad residue/molecule data in prmtop!
> | Residue 739(atoms 11384- 11398) is in multiple molecules.

Thanks for the report. It certainly does look like LEaP is setting up an
incorrect list of "molecules". The ambpdb program (but not LEaP itself) uses
this list to figure out where to place the TER cards in the output file. And,
pmemd (but not sander) checks this for consistency with the residue list.

Can you post the pdb file and the LEaP commands you used? As Bob Duke pointed
out, we haven't run across this problem very much (if at all). But if we can
reproduce the problem, we can probably track down what is going on.

...thanks...dac

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