Re: [AMBER] Converting Amoeba .xyz for use with Amber

From: Eugene Yedvabny <>
Date: Fri, 13 Dec 2013 14:08:40 -0800

Hi Amber community,

I am still stuck with Amber -> Tinker -> Amber conversion necessary to get
Amoeba prmtop and inpcrd. It appears that my first assumption about NHE ->
NH2 conversion being the culprit is wrong. The error is actually caused by
the disulfide bridge: Tinker recognizes CYX residues and automatically
makes a bond between them (yay!) but then analyze.x chokes on the
multipoles for that bridge (nay!):

Atomic Multipole Parameters :

            Atom Coordinate Frame Definition Multipole Moments
2 2 0 0 0.00000
                                                  0.00000 0.00000 0.00000
                                                  0.00000 0.00000
                                                  0.00000 0.00000 0.00000

I am attaching the whole analout file, but the above is an example of a
section that confused tinker_to_amber.

I tried changing CYX to CYS manually in the PDB, but Tinker is smart enough
to recognize a SS bond and auto-converts it back to CYX, leading to the
error. If I feed in an extended chain of the same peptide (oxytocin), where
the CYS residues are too far apart to bond, the weird multipole sections go
away and the analout file is parseable by tinker_to_amber.

Have any of you come across this type of issue before? Is this an artifact
of Tinker 6, or are disulfide bridges not really supported for
Tinker->Amber conversion?

I will also try to ask the Tinker community whether they've come across
something similar.

Thank you,
Eugene Yedvabny

On Mon, Dec 9, 2013 at 2:27 PM, Eugene Yedvabny <>wrote:

> I am attaching my test files for your reference. The oxy_stripped.pdb is
> what was generated with cpptraj and oxy.pdb is my edited version with NHE
> -> NH2. You would need to change the path in the key file to point to your
> install of Tinker, but everything else should be generic.
> Thank you,
> Eugene Yedvabny
> ------------------------------
> From: Eugene Yedvabny Eugene Yedvabny <>
> Reply: Eugene Yedvabny
> Date: December 9, 2013 at 2:24:39 PM
> To:
> Subject: Converting Amoeba .xyz for use with Amber
> Hello Dr. Case and Dr. Swails,
> Sorry for the out-of-order reply; my mailing-list subscription was
> apparently disabled and I can't seem to directly reply to your responses.
> I've sort-of figured out the root of my issue, but now am stuck on how to
> best resolve it. My Amoeba simulation was run on Oxytocin, built with
> AmberTool 13 tleap. Oxytocin is a capped protein with the NHE group as the
> 10th residue. Tinker, however, doesn't understand the NHE code and so I
> manually changed the residue code to NH2 in the pdb I generated with
> cpptraj. This made the pdb recognizable to Tinker's pdbxyz and analyze, but
> clearly screws something up with respect to tinker_to_amber reading the
> resulting analout (the numf=5 error). I also have a disulfide bridge
> between residues 1 and 6, but since both Amber and Tinker support CYS/CYX
> codes and bridge-making, I don't imagine that being the problem.
> I've ran all the steps with a tleap-modeled Bradykinin and was able to
> generate working prmtop + inpcrd with Tinker 6.2 and Amber 12's
> tinker_to_amber. So I think the issue has to do with my NHE -> NH2 mod.
> I am sure I am not the first person to attempt running capped peptides
> in Tinker, and yet I can't seem to find what others have done with respect
> to Tinker's handling of NHE/NH2. Have you come across this issue before,
> and if so, what would be the best resolution?
> Thank you,
> Eugene Yedvabny

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Received on Fri Dec 13 2013 - 14:30:02 PST
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