[gmx-users] Simulation of the HEM-containing proteins

Wed Apr 3 16:31:27 CEST 2013

On Wed, Apr 3, 2013 at 10:27 AM, James Starlight <jmsstarlight at gmail.com>wrote:

> I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but
> after processing that structure to grompp I've obtained errors like
>
> ERROR 1 [file topol.top, line 2106]:
>   No default Bond types
>
>
> ERROR 2 [file topol.top, line 2144]:
>   No default Bond types
>
>
> ERROR 3 [file topol.top, line 3153]:
>   No default Bond types
>
>
> ERROR 4 [file topol.top, line 8725]:
>   No default U-B types
>
>
> ERROR 5 [file topol.top, line 8792]:
>   No default U-B types
>
>
> ERROR 6 [file topol.top, line 10624]:
>   No default U-B types
>
>
> ERROR 7 [file topol.top, line 10625]:
>   No default U-B types
>
>
> ERROR 8 [file topol.top, line 11382]:
>   No default U-B types
>
>
> ERROR 9 [file topol.top, line 11383]:
>   No default U-B types
>
>
> ERROR 10 [file topol.top, line 11384]:
>   No default U-B types
>
>
> ERROR 11 [file topol.top, line 11385]:
>   No default U-B types
>
>
> ERROR 12 [file topol.top, line 11491]:
>   No default U-B types
>
>
> ERROR 13 [file topol.top, line 11492]:
>   No default U-B types
>
>
> ERROR 14 [file topol.top, line 11493]:
>   No default U-B types
>
>
> ERROR 15 [file topol.top, line 11506]:
>   No default U-B types
>
>
> ERROR 16 [file topol.top, line 11507]:
>   No default U-B types
>
>
> ERROR 17 [file topol.top, line 11508]:
>   No default U-B types
>
>
> ERROR 18 [file topol.top, line 12147]:
>   No default Proper Dih. types
>
>
> ERROR 19 [file topol.top, line 12148]:
>   No default Proper Dih. types
>
>
> ERROR 20 [file topol.top, line 12149]:
>   No default Proper Dih. types
>
>
> ERROR 21 [file topol.top, line 12150]:
>   No default Proper Dih. types
>
>
> ERROR 22 [file topol.top, line 12151]:
>   No default Proper Dih. types
>
>
> ERROR 23 [file topol.top, line 12152]:
>   No default Proper Dih. types
>
>
> ERROR 24 [file topol.top, line 12247]:
>   No default Proper Dih. types
>
>
> ERROR 25 [file topol.top, line 12248]:
>   No default Proper Dih. types
>
>
> ERROR 26 [file topol.top, line 12249]:
>   No default Proper Dih. types
>
>
> ERROR 27 [file topol.top, line 12250]:
>   No default Proper Dih. types
>
>
> ERROR 28 [file topol.top, line 12251]:
>   No default Proper Dih. types
>
>
> ERROR 29 [file topol.top, line 12252]:
>   No default Proper Dih. types
>
>
> ERROR 30 [file topol.top, line 14948]:
>   No default Proper Dih. types
>
>
> ERROR 31 [file topol.top, line 14950]:
>   No default Proper Dih. types
>
>
> ERROR 32 [file topol.top, line 14952]:
>   No default Proper Dih. types
>
>
> ERROR 33 [file topol.top, line 14956]:
>   No default Proper Dih. types
>
>
> ERROR 34 [file topol.top, line 14957]:
>   No default Proper Dih. types
>
>
> ERROR 35 [file topol.top, line 14958]:
>   No default Proper Dih. types
>
>
> ERROR 36 [file topol.top, line 14959]:
>   No default Proper Dih. types
>
>
> ERROR 37 [file topol.top, line 14960]:
>   No default Proper Dih. types
>
>
> ERROR 38 [file topol.top, line 14961]:
>   No default Proper Dih. types
>
>
> ERROR 39 [file topol.top, line 14962]:
>   No default Proper Dih. types
>
>
> ERROR 40 [file topol.top, line 14963]:
>   No default Proper Dih. types
>
>
> ERROR 41 [file topol.top, line 14964]:
>   No default Proper Dih. types
>
>
> ERROR 42 [file topol.top, line 14965]:
>   No default Proper Dih. types
>
>
> ERROR 43 [file topol.top, line 14966]:
>   No default Proper Dih. types
>
>
> ERROR 44 [file topol.top, line 16263]:
>   No default Proper Dih. types
>
>
> ERROR 45 [file topol.top, line 16264]:
>   No default Proper Dih. types
>
>
> ERROR 46 [file topol.top, line 16269]:
>   No default Proper Dih. types
>
>
> ERROR 47 [file topol.top, line 16270]:
>   No default Proper Dih. types
>
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 3 [file topol.top, line 16745]:
>   System has non-zero total charge: 7.000001
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
> -------------------------------------------------------
> Program grompp, VERSION 4.6
> Source code file:
> /home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line: 1593
>
> Fatal error:
> There were 47 errors in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> During visualization of the complex.gro file I didnt observe any
> distortions in the geometry of heme-cytochrome complex (it looks like NMR
> structure) but why that errors occured ?
>
>
Heme is tricky, and this error comes up every time someone tries to use
heme in Gromacs (see the archive for tips and possible solutions).
 Parameters are missing for bonded interactions, so either add them
directly to the .top or to ffbonded.itp.  You'll have to search the
literature for suitable parameters or derive them yourself.  There are lots
of reports of heme-containing proteins being simulated, so clearly the
fully parameter set exists somewhere.

-Justin

-- 

========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================