Re: [AMBER] CPPTRAJ parameter file error

From: Daniel Roe <>
Date: Wed, 2 Oct 2019 09:31:48 -0400


On Tue, Oct 1, 2019 at 6:36 PM Rui Chen <> wrote:
> I uploaded a parameter file into CPPTRAJ. I got the following errors. I
> double checked the atom numbering is sequential. It seems like the problem

It's not that atom numbering is sequential - it's that the atom range
in the molecule is not completely contiguous. So something like this:

Molecule 1: Atoms 1 2 3 4 10 11 12 13
Molecule 2: Atoms 5 6 7 8 9

Cpptraj (and I think other programs in Amber as well) operates on the
assumption that molecules are completely contiguous (this is
beneficial for a lot of reasons). When they aren't, cpptraj kicks back
this error. I think parmed will give you a similar warning.

> Just to let you know, this is a homodimer and the following mentioned atom
> 6615 is the first atom of the glycans. I think the problem is the
> glycan/protein interactions. I tried the four ways mentioned in the first
> snapshot, none of them worked.

Can you elaborate on *exactly* what you did and describe exactly why
it didn't work? We need way more information to help.


> Could you please give me some clues? Looking forward to your reply.
> [image: Screen Shot 2019-10-01 at 3.45.59 PM.png]
> [image: Screen Shot 2019-10-01 at 3.47.01 PM.png]
> Best regards,
> Rui
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Received on Wed Oct 02 2019 - 07:00:02 PDT
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