From: David A Case <>
Date: Tue, 28 Jul 2020 09:59:16 -0400

On Tue, Jul 28, 2020, 辛志宏 wrote:

>I process the box boundry using equil trajectory mdcrd file to generate
>a correspoding nc file due to a partition of water moleculare out of
>box after equilation, and then open the nc file in the vmd, and select
>parameters "save coordinate,fist 499, last 499, stride 1" and save as
>DLF-equil-499.pdb file as QM/MM inuptfile (but box is gone from here)
>when the runing box stop, and then a new prmtop and incrd were generated
>from DLF-equil-499.pdb, I presume this is the case where the issue
>occured, but I do not know how to fix the issue, please help me, thank

oooh...just use cpptraj for all of this!

First, if it is a problem that water molecules are "out of the box" use the
autoimage action in cpptraj to pack things back in. Then you can save the
file as a restart file, also in cpptraj. There should be no reason to need to
recreate a prmtop file here: all you have done is change the coordinates of
some atoms. I'm not sure what you mean by the phrase "QM/MM inputfile", or
why you what a PDB-format file.

If you (for whatever reason) get a PDB-format file as an intermediate, you
will need to manually add back in the box parameters in the tleap step, after
your loadPdb command. Type "help set" and look for box information.


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Received on Tue Jul 28 2020 - 07:00:05 PDT
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