[gmx-users] amb2gmx for big systems

Alan alanwilter at gmail.com
Fri Aug 1 09:55:12 CEST 2008

Dear Rebeca,

I modestly build a program based on antechamber and inspired mostly by


I hope it can be a bit easier to use. You should also take a look in
the tutorials I put there, because the may give you an idea why you
are facing problems (I suspect your lipid.itp is in the wrong place of
the top file). And it also may help you to better set up ffamber in

Moreover, it seems you're using amber atom types instead of gaff atom
types (did you use antechamber right?). I would suggest you to use
gaff atom type. Or try just to delete the [ atomtypes ] field and pray
that the ffamber## ff you took in GROMACS will handle it.


On Thu, Jul 31, 2008 at 7:34 PM,  <gmx-users-request at gromacs.org> wrote:
> Hello,
> I am trying to translate the amber topology for a system membrane+protein (dry) to Gromacs. In view of the problems caused in amb2gmx.pl due to the size of the system (more than 600.000 atoms) I had tried another alternative:
> I created the amber topology for the protein and for a unique lipid molecule separately and I converted them to gromacs using amb2gmx.pl (now, no problems were found, as is logic). Then, from the gromacs topologies, I construct the .itp files for the protein and lipid, removing the correspondent lines and putting them into another file that I have called amberff.itp
> However, several atomtypes for the lipid are the same than those for the protein, and they have nothing to do between them:
> [ atomtypes ];name  bond_type    mass    charge   ptype          sigma      epsilonO              O      0.0000  0.0000  A   2.95992e-01  8.78640e-01H1            H1      0.0000  0.0000  A   2.64953e-01  6.56888e-02N3            N3      0.0000  0.0000  A   3.25000e-01  7.11280e-01O2            O2      0.0000  0.0000  A   2.95992e-01  8.78640e-01HA            HA      0.0000  0.0000  A   2.64953e-01  6.56888e-02HC            HC      0.0000  0.0000  A   2.64953e-01  6.56888e-02C              C      0.0000  0.0000  A   3.39967e-01  3.59824e-01CT            CT      0.0000  0.0000  A   3.39967e-01  4.57730e-01HP            HP      0.0000  0.0000  A   2.64953e-01  6.56888e-02
> and I am getting errors in grompp due to this fact.
> Does anybody has any idea to solve this?

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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