Re: [AMBER] problem setting up an amber simulation

From: David A Case via AMBER <>
Date: Sun, 22 Jan 2023 12:45:29 -0500

On Sat, Jan 21, 2023, laura zhang via AMBER wrote:

>I tried to use cpptraj's prepareforleap to do the work.
>did your original pdb file have hydrogen atoms? the names in the error messages appear to be non-standard.

I'm not sure that prepareforleap will correct errors in the atom names in
your original PDB file. There are a lot of these, and I'm guessing(?) that
this came from CHARMM (especially since the CD atom of ILE is incorrect).

Where did this PDB file come from in the first place? If CHARMM or the
CHARMM-gui is involved, see if there is not an option to get standard atom
names into the file.

If you can't do that, try using pdb4amber to remove all the hydrogens, and
use a text editor to replace CD in ILE with CD1. That should get you much
closer to an input file that matches the PDB/IUPAC standard, which is what
Amber follows.

...good luck...dac

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Received on Sun Jan 22 2023 - 10:00:02 PST
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