AMBER Archive (2006)

Subject: Re: AMBER: erroneous placement of TER card

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Nov 16 2006 - 10:47:23 CST

Dave -
I have actually worked with a couple of users on this sort of problem over
maybe the last 3 years or so, and it was briefly discussed on the list; it
is infrequent that someone hits this though, and I think it generally has to
do with them crofting up a residue and / or adding a bond to a cofactor or
something, and possibly how things are located in the pdb. I think the
folks I worked with basically just found the correct way to not mislead
leap, and moved on, so I never figured out the details as to how things go
wrong. Hopefully we will have the next version a little more tightly
specified so that this is harder to do, but it is outside my area of
expertise, so I have just tried to do my best to get them going again.
Certainly getting xleap et al. behaviour with TER cards cleared up can't
hurt, though.
Best Regards - Bob
----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, November 16, 2006 11:20 AM
Subject: Re: AMBER: erroneous placement of TER card

> 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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