[gmx-users] Re: problems running grompp with protein-ligand complex

Alan alanwilter at gmail.com
Thu Dec 4 10:39:22 CET 2008

Dear Fabricio,
It's not only you who is confused here...

So, I will try to help the best I can and sorry if I ask you redundant
questions you've likely answer before. It happens that I read GMX mailing
list in digest mode.

BTW, when replying gmx list, cc to my email (alanwilter _at gmail . com) and
so you can have a prompt reply.

AFAIU, you have a protetin (receptor.itp?) and a ligand, right? And your
ligand is not covalently bond to the protein, isn't it?

If so, have you see this?:


Have you seen this note?:

*NB(1):* #include "Ligand.itp" has to be inserted right after
ffamber**.itp line
and before Protein_*.itp line in *Complex.top*.

It seems that you missing the difference between *.top and *.itp files. So,
as Justin said, read chapter 5 of GMX manual.

Another alternative, if you pretty familiar to AMBER and tleap is to build
your system there and once you have your prmtop and inpcrd files, use acpypi
to convert them to GMX files and put run EM and MD.

If all I am saying here is still not helping, consider to send me your input
PDB file (protein and complex) and let me run it here.

Just one more thing, would you mind where are you from and what's your

Many thanks in advance,


On Thu, Dec 4, 2008 at 04:01, <gmx-users-request at gromacs.org> wrote:

> I am working with a system using ffamber99 forcefield and trying to
> set up a ligand protein complex system. I have encountered some
> problems with grompp now.
> In my past email, the problem was that : > Fatal error: Found a second
> defaults directive, file "ligand.itp", line 5. Then the following
> solution was given:
> " You have to combine all atomtypes into one file something like
> filename ff_atomtypes.itp
> #define FF_ATOMTYPES
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
> [ atomtypes ]
> ; name        mass      charge    ptype               sigma
> epsilon
>     S       0.0000  0.0000  A   3.56359e-01  1.04600e+00
>   CC      0.0000  0.0000  A   3.39967e-01  3.59824e-01
>   HO      0.0000  0.0000  A   0.00000e+00  0.00000e+00
>   N3      0.0000  0.0000  A   3.25000e-01  7.11280e-01
> all atom types from amber force field 99 and also from your ligand (check
> if
> parameters are ok).
> delete atomtypes and defaults entry in your ligand.itp
> load in your .top
> #include "ff_atomtypes.itp"
> #include "receptor.itp"
> #include "ligand.itp"
> "
> I tried to do this and ended up with the following .top file:
> ; 15d-pgj2_GMX.top created by acpypi on Wed Dec  3 14:10:55 2008
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
> ; Include 15d-pgj2_GMX.itp topology
> #include "15d-pgj2_GMX.itp"
> [ system ]
>  15d-pgj2
> [ molecules ]
> ; Compound        nmols
>  15d-pgj2         1
> And all the atomtypes are in the 15d-pgj2_GMX.itp, which is too big to
> put here. But is present in past posts.
> Ok, so no grompp tells me the same error it did before. Fatal error:
> Found a second defaults directive, file "15d-pgj2_GMX.top"
> When I substitute the 15d-pgj2_GMX.top for the 15d-pgj2_GMX.itp in my
> protein.top grompp gives out the following error:
> Fatal error:No such moleculetype PJ2
> Now I am quite confused and would like some advice on the matter.
> Thank you
> Fabrício Bracht
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081204/f78c84fd/attachment.html>

More information about the gromacs.org_gmx-users mailing list