AMBER Archive (2009)

Subject: Re: [AMBER] How to remove Hydrogen using ptraj

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Tue Sep 01 2009 - 12:25:10 CDT

> > Note also that if you have 4-letter hydrogen names, typically the 4th
> > character is wrapped so you might also want to add:
> >
> > strip @?H*
>
> Is this true? Does ptraj not use the atom names in the prmtop file?
>
> Fortunately, with pdb format version 3, there is no longer any "wrapping" of
> hydrogen names in PDB files, so this problem should go away.

Since ptraj can read the older PDB formats (not just prmtop or PSF files)
to get names, this can be true, but you are correct that if a prmtop is
specified, the names in the prmtop are correctly applied. --tom

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