Re: [AMBER] problem setting up an amber simulation

From: Daniel Roe via AMBER <>
Date: Sun, 22 Jan 2023 12:58:55 -0500

On Sun, Jan 22, 2023 at 12:45 PM David A Case via AMBER
<> wrote:
> 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

'prepareforleap' is mostly set up to correct sugar atom/residue names,
but stuff like this (i.e. changing a.a./n.a. residue/atom names) may
be added in the future. For now if using 'prepareforleap' use the
'noh' keyword to remove hydrogens (leap will build them back in) and
prior to 'prepareforleap' use the 'change' command to change the ILE
atom names, e.g.

parm mypdb.pdb
loadcrd mypdb.pdb name MyPdb
change crdset MyPdb atomname from :ILE.CD to CD1
prepareforleap crdset MyPdb noh <other prepareforleap options> pdbout
cpptraj.pdb out

Hope this helps,


> 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 - 10:00:03 PST
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