You need to use the autoimage command if you want to autoimage.
On Sun, Nov 12, 2023, 1:40 AM Singh,Ravi via AMBER <amber.ambermd.org>
wrote:
> Hello,
> The create .mdcrd file I used below command.
>
> trajin md.nc 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 <dacase1.gmail.com>
> Sent: 12 November 2023 02:46
> To: Singh,Ravi <ravi_comp.chem.22.gm.gist.ac.kr>
> 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,
> amber.ambermd.org,
> 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
> http://lists.ambermd.org/mailman/listinfo/amber for information on how to
> subscribe.
>
> >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
> >75×75×75. 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.
>
> ...dac
>
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Received on Sun Nov 12 2023 - 04:00:04 PST
