Re: [AMBER] error in creating prmtop and inpcrd files

From: Jason Swails <>
Date: Sun, 13 Mar 2011 14:55:13 -0700

Hi Chris,

Ben is exactly correct, but I'll add to it some. Leap works based on force
field templates, such as the OFF library files that Ben pointed you to (You
can see a description of this file format on both OFF files and amber Prep
files); so the atom names in your PDB must
match the atom names provided in the template files for those residues.

The atom naming scheme in LEaP follows the atom naming scheme found in the
current version of the PDB standard (which is obviously intentional). This
makes sure that most standard PDBs that don't have specialized cofactors of
any kind will work without any modification. This leads me to believe that
you got your PDB file somewhere else (or had another program add hydrogen
atoms to it).

The easiest way to solve this is, as Ben said, strip H atoms from your PDB
file and let LEaP add them back. You can do this via the program "reduce"
using the -Trim flag.

reduce -Trim input_pdb > output_pdb

You can also use reduce to add the hydrogens back in if you don't want to
use the locations LEaP puts them in (which are typically fine).

Hope this helps,

On Sun, Mar 13, 2011 at 2:34 PM, Ben Roberts <> wrote:

> Hi Chris,
> On 13/03/2011, at 4:55 PM, Chris Bryant wrote:
> > Seems like it is all of them. Here is the file I am working with. Does
> this answer your question?
> Thanks for the clarification. I don't think the problem is all the atoms;
> for example, in your logs, it complains about ARG 361 HB1, ARG 361 HG1, ARG
> 361 HD1, etc. Notably, however, HB2, HG2, HD2, etc. don't trigger the same
> complaint. This is because, for example, LeAP expects hydrogens on CB in ARG
> residues to be named HB2 and HB3, instead of HB1 and HB2 (and likewise for
> hydrogens attached to other heavy atoms).
> If I understand correctly, LeAP expects very specific atom names in its
> residues when assigning atom types. If your atoms aren't named according to
> the entries in the residue topology libraries, it won't be able to address
> them.
> The official atom naming scheme can be found in the file:
> $AMBERHOME/dat/leap/lib/all_amino94.lib (for intra-chain amino acids)
> $AMBERHOME/dat/leap/lib/all_aminoct94.lib (for C-terminal amino acids)
> $AMBERHOME/dat/leap/lib/all_aminont94.lib (for N-terminal amino acids)
> One possible approach is to fix the hydrogen atom names by hand (for
> example, in residue 361, replacing HB1 and HB2 with HB2 and HB3
> respectively, and so on). However, I don't recommend this given that it's
> very time-consuming. Another is to throw away all hydrogen atoms from your
> PDB and let other programs add them for you. I think leap should be able to
> add correctly named hydrogen atoms automatically given a heavy-atom
> skeleton; if not, check out "reduce", which is bundled with AmberTools.
> Good luck!
> Ben
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sun Mar 13 2011 - 15:00:04 PDT
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