Re: [AMBER] tLeap adding non-library hydrogens

From: Huang Jing <>
Date: Sat, 7 Jan 2017 14:41:52 +0200

As David Case suggested, "pdb4amber" command is needed to change any kinds
of pdb files to amber format;

the parameters of the standard residues are well fitting and missing atoms
are created automatically when the pdb file is loaded;

For those non-standard molecules, the .mol2 and .frcmod files are required.
If you wanted to creat the .mol2 and .frcmod files by using antechamber,
the pdb coordinate with missing atoms is needed;
what I do is to extract the coordinate of non-standard molecule (without
missing atoms) from the pdb file of protein and then add missing atoms by
graphic interface;
later, use antechamber to generate the mol2 and frcmod files and change the
coordinate of the non-standard molecule with the whole coordinate
(including the missing atoms) in the pdb file of protein;
finally run the tleap to generate .prmtop and .inpcrd files.


On Sat, Jan 7, 2017 at 2:07 PM, David Poole <> wrote:

> Hello Huang,
> There were in fact errors but it seems to be that the pdb file is to
> blame. Like so many before there were simply inconsistencies in the
> naming of the individual atoms.
> That said.. tleap made no errors, entirely user generated.
> Now, having established the problem, I'd like to ask another question
> in general about tleap, specifically, how does it assign the location
> of missing atoms for library or added molecules?
> -David
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Received on Sat Jan 07 2017 - 05:00:03 PST
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