Re: [AMBER] Problem in saving parameter/topology and coordinate file.

From: David A Case <>
Date: Tue, 21 Jul 2015 06:53:08 -0600

On Mon, Jul 20, 2015, Harshala Haldankar wrote:

> > According to the tutorial, I had used charmm gui to build the
> > protein/membrane system. Later I converted it to amber compatible format
> > using script. I used *leaprc.lipid11 *force field
> > for lipid bilayer and *leaprc.ff12SB* force field for my peptide. When I
> > try to save parameter/topology and coordinate file, it gives error as
> > follows:
> > "does not have a type"

This generally means that you have an atom in your input PDB file whose atom
name and residue name do not correspond to those in the library you have

I'm not sure what CT3 is, but Amber libraries have no such terminal residues.
You will have to modify your peptide to use one of the Amber C-terminal
capping residues (NME or NHE), or create your own library file (quite a bit
harder to do, but certainly possible.)

...hope this helps....dac

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Received on Tue Jul 21 2015 - 06:00:04 PDT
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