Re: [AMBER] Regarding maximum molecular system size

From: Singh,Ravi via AMBER <>
Date: Sun, 12 Nov 2023 06:40:26 +0000

The create .mdcrd file I used below command.

trajin 1 10000 10
trajout md_1.mdcrd crd

I am not aware if it is autoimage.
However upon looking inside those created files I get below coordinates. Box size 74*74*75
>Cpptraj Generated trajectory
>-416.730-101.326 -63.637-416.090-100.840 -62.850-416.804-100.678 -64.539-416.217
Is there a better way to create mdcrd file from .nc files ??

From: David A Case <>
Sent: 12 November 2023 02:46
To: Singh,Ravi <>
Subject: Re: [AMBER] Regarding maximum molecular system size

On Sat, Nov 11, 2023, Singh,Ravi wrote:
>Hello David,

Please send amber-related questions to the mail reflector,,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See for information on how to

>I have a molecular system of 37,500 atoms(water 10,000 and butanol
>500). But I received weird coordinates. The box size was around
>757575. However, I expect all my simulated molecules to be within those
>dimensions. For reference I will paste few lines of the coordinates which I
>received. Even the pdb file obtained the number of molecules ended on 9999
>and started from 0. Please have a look at the coordinates.
>Cpptraj Generated trajectory
>-416.730-101.326 -63.637-416.090-100.840 -62.850-416.804-100.678 -64.539-416.217

As a wild guess, this might be an imaging problem. Have you used autoimage
in cpptraj to pack things back into a single unit cell?

The pdb format does not permit more than 10,000 residues, since the residue
number column is only 4-characters wide. This is only a problem with that
format, and (depending on use) is often not a problem. The limitation has
nothing to do with Amber, but with an limited (and deprecated) format that
was created in the 1970's.


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Received on Sat Nov 11 2023 - 23:00:03 PST
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