Re: [AMBER] CL topology

From: Jason Swails <>
Date: Wed, 19 Aug 2015 07:42:02 -0400

On Wed, Aug 19, 2015 at 3:04 AM, Albert <> wrote:

> Hello:
> I am using acpype to create ligand topology. However, I noticed that
> acpype may not recogonize Cl element which is a halogen atom correctly.
> After acpype, it generate a new ligand pdb file called: lig_NEW.pdb and
> I found the following:
> ATOM 10 C09 UNK Z 1 11.502 -10.939 3.783 1.00
> 0.00 C
> ATOM 11 CL11 UNK Z 1 10.314 -10.335 4.933 1.00
> 0.00 C
> ATOM 12 C12 UNK Z 1 12.865 -10.938 4.098 1.00
> 0.00 C
> ATOM 13 CL13 UNK Z 1 13.389 -10.333 5.666 1.00
> 0.00 C
> atom CL11 and CL13 are halogen atom, but it seems that acpype treat them
> as carbon which is wrong.... I am just wondering how can we solve this
> problem?

‚ÄčThis is the wrong place to ask for help about acpype -- as I mentioned in
a post here yesterday, Amber developers are unlikely to convert an Amber
topology for use with Gromacs. We are just going to use the Amber MD
engines. So it is very likely that nobody frequently responding here will
have ever used acpype before.

If this problem happened to me, I would first try and make sure that the
problem was acpype and not antechamber -- that is, make sure that a prmtop
file generated by antechamber actually assigned the atomic number of the CL
atoms to 17 and not 6. If that was correct, I would look through the
acpype manual and see if there was some option that looked like it would
help here. If the answer wasn't available there, I would then try and
check the acpype source code.

Another option is to use a developmental version of ParmEd, which has the
ability to convert between Amber and Gromacs topologies. This Github issue
contains some instructions for doing so:

Note that you *must* use the developmental version of ParmEd from Github
(not the version included with AmberTools 15), since it is a very new


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Aug 19 2015 - 05:00:03 PDT
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