[gmx-users] Re: Problem of lipid-protein simulation

[chris.neale at utoronto.ca]

Dear Kamalesh, please post this to the mailing list instead of
sending it directly to me. Once you post it to the list, I am fairly
likely to respond for membrane questions. When you post to the list,
though, you also have the chance of getting input from somebody else, and
also some form of quality control in that other people read the answers
and may suggest corrections if needed.

Chris.

Quoting Kamalesh Roy <roy.kamalesh at gmail.com>:

> Dear Sir,
>
> I am the new user in gromacs, I am using the gromacs-3.3.1 version of that..
>
> I have simulated a peptide in a water box using ffG43a1.itp force
> field with out neutralising my system I faced no problem.
> And also I have used ffgmx.itp to equilibrate my bilayer (DPPC) the
> energy and area is satisfactory.
>
> But now I want to use the equilibrated bilayer and the peptide
> (simulated in water) together.
> I have inserted the peptide in the bilayer and made a pdb.
> In my pdb file the serial of the coordinates are protein, DPPC, Sol
>
> then I am using the .top file like the following..
> ------------------------------------------------------------------
> #include "ffG43a1.itp"
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "dppc.itp"
> #include "ions.itp"
>
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
> [ system ]
> ; name
> Neurokinin B in DPPC
>
> [ molecules ]
> ; name  number
> Protein 1
> DPPC    128
> SOL     3655
> --------------------------------------------------------------------------
>
> whenever I am running the grompp there are sevesral warning for over
> writting the atomtype
> and last the fatal error showing the following...
>
>
> last two warnings I am giving here along with the error.
>
>
> -----------------------------------------------------------------------------------------------------------------------
> WARNING 241 [file "/usr/local/gromacs/share/gromacs/top/ffgmxbon.itp",
> line 710]:
>   Overriding Proper Dih. parameters,
>   old: 0 2.93 3 0 0 0
>   new: S CH2 1 0.000 2.929 3
>
> WARNING 242 [file "/usr/local/gromacs/share/gromacs/top/ffgmxbon.itp",
> line 711]:
>   Overriding Proper Dih. parameters,
>   old: 0 16.7 2 0 0 0
>   new: S S 1 0.000 16.736 2
>
> Generated 2259 of the 4005 non-bonded parameter combinations
> Cleaning up temporary file gromppdbbEuU
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 754
>
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1
>
> -------------------------------------------------------
>
> "Whatever Happened to Pong ?" (F. Black)
> --------------------------------------------------------------------------------------------------------------------------
>
> Do I need to neutralise the system first to insert the atoms as in the
> top file...
>
> I am confused with the problem please help me....
> Thank You in advance..
>
>
> Kamalesh Roy
> Department of chemistry
> Raja Bazar Science Collage, Kolkata
> India.
>