[gmx-users] editbox removes dummy atoms

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Thu Jun 28 16:40:37 CEST 2012

I have found out that there was always the same residue number for all the
dummy atoms. Perhaps that was the failure. Now I changed it so that they
have all different residue numbers. But now I get the error:

Atom N is used in an interaction of type improper in the topology
database, but an atom of that name was not found in residue
number 309.

when I want to put hydrogens to the structure.

pdb2gmx -f 3m71_mod.pdb -o 3m71.gro -p 3m71.top -water tip3p -ff amber03 2>>l
ogErr 1>>logOut

> On 6/28/12 10:11 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I have an protein structure with many dummy atoms around it simulating
>> the
>> membrane around the protein. Those dummy atoms are signed in the file as
>> an ATOM.
>> When I want to put this protein with the membrane in a box with the
>> command
>> editconf -f 3m71.gro -o 3m71_box.gro -bt dodecahedron -d 1.0 2>>logErr
>> 1>>logOut
>> it removes the membrane dummy atoms except of one Dummy atom. How can
>> that
>> be.
>> What do I have to change?
> Does the second line of the .gro file specify the correct amount of atoms?
>  The
> only reason I know of that editconf will truncate the file is if this line
> is
> incorrect.
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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