On 22/03/2012 1:46 AM, francesco oteri wrote:
Dear gromacs user,
I noted a strange behavior in topology generation workflow.
I have a protein whose active site contains a Ni atom linked to 4 Cys.
I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I have
inspected
the Linking messages and they fit with the expected topology, I mean
pdb2gmx
correctly detects the four bonds nickel-sulphur.
So I run grompp and the topol.tpr has been correctly generated.
Then I compared topol.top and topol.tpr bonds and I noticed that in
topol.top there a lot
of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium.
Can you show an example of what you interpret as a fake bond?
Mark
I dumped topol.tpr through gmxdump, and I noticed that these bonds are
no more present
and only "right" bonds are present.
So, I am wondering why the fake bonds are inserted in topol.top and
how grompp detectes
these bonds.
Francesco
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
