Re: [AMBER] Problems during solvation of molecule from Protein Data Bank

From: Sowmya Indrakumar <>
Date: Tue, 13 Dec 2016 11:05:03 +0000

You can try to have the structure in the amber pdb format and then try to solvate
Try this : pdb4amber -i input structure -o output.pdb -y

From: David A Case []
Sent: Tuesday, December 13, 2016 2:52 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Problems during solvation of molecule from Protein Data Bank

On Mon, Dec 12, 2016, The Cromicus Productions wrote:
> I'm trying to solvate the molecule 1S2R in tLeap but I'm getting the
> following errors:
> FATAL: Atom .R<SPM 25>.A<N1 1> does not have a type.

Just to add to what Carlos said: a more general answer to this type of

A reminder: tleap is really just a bookkeeping program: it reads in libraries
of residues/molecules (called units) that Amber knows about. Then it
just tries to match residue and atom names in the input pdb file with those
in the library. It doesn't know any chemistry, or what anything "means": it
just matches these things up.

At any point, you can use the "list" command to see what units tleap knows
about, i.e. what units have been loaded into its memory. Unless that list
shows the residue SPM, it won't be able to process a pdb file that has an SPM

If you have a non-standard residue, like SPM, the usual (although by no means
only) way to proceed is to first build the library using antechamber. The
R.E.D. website is another popular service that can help you to do this.
Or, a Google search on "amber spermine parameters" will give you pointers
to how others have done similar calculations.

So, although tleap is the program that is reporting the error, your real
problem probably lies in the lack of an Amber library file that describes

...hope this helps...dac

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