[gmx-users] Generating topology for a HEM protein with CHARMM27

[Justin Lemkul]

On 5/23/16 5:31 AM, zeineb SI CHAIB wrote:
> I'm looking to generate the topology of a HEM protein , I choose CHARMM as a force field. At the begining, when I run pdb2gmx I had this error about missing hydrogen's:
>
> WARNING:
> atom HA is missing in residue HEM 473 in the pdb file
>
>         You
> might need to add atom HA to the hydrogen database of building block
> HEME
>
>         in
> the file aminoacids.hdb (see the manual)
>
>
>
>
>
>
> WARNING:
> atom HB is missing in residue HEM 473 in the pdb file
>
>         You
> might need to add atom HB to the hydrogen database of building block
> HEME
>
>         in
> the file aminoacids.hdb (see the manual)
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------
> Program
> pdb2gmx, VERSION 4.6.5
> Source
> code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line:
> 1588
>
>
>
> Fatal
> error:
> There
> were 30 missing atoms in molecule Other2, if you want to use this
> incomplete topology anyhow, use the option -missing
> For
> more information and tips for troubleshooting, please check the
> GROMACS
> website
> at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> After a research, I found what was missing: I made a copy of aminoacids.hdb (Charmm27.ff folder) in my working directory and I edited this file:
> I added the following Lines:
>

The .hdb file must still be in the force field directory (wherever that may be, 
$GMXLIB or working directory), not in the working directory itself.  Otherwise 
it will have no effect.

>
>
>
> 	
> 	
> 	
> 	
>
>
>
> HEME 16
>
> 1
>       1       HA
>      CHA     C1A     C4D
> 1
>       1       HB
>      CHB     C4A     C1B
> 1
>       1       HC
>      CHC     C1C     C4B
> 1
>       1       HD
>      CHD     C1D     C4C
> 3
>       4       HMA
>     CMA     C3A     C2A
> 2
>       6       HAA
>     CAA     C2A
>     CBA
> 2
>       6       HBA
>     CBA     CAA
>     CGA
> 3
>       4       HMB
>     CMB     C2B     C1B
> 1
>       1       HAB
>     CAB     C3B     CBB
> 2
>       3       HBB
>     CBB     CAB     C3B
> 3
>       4       HMC
>     CMC     C2C     C1C
> 1
>       1       HAC
>     CAC     CBC     C3C
> 2
>       3       HBC
>     CBC     CAC     C3C
> 3
>       4       HMD
>     CMD     C2D     C1D
> 2
>       6       HAD
>     CAD     C2D     CBD
> 2
>       6       HBD
>     CBD     CAD     CGD
>
>
>
> I fixed the problem of missing hydrogens but I'm having another type of error:
>
> Special Atom Distance matrix:
>                   HEM360  HEM360
>                     CAB2    CAC3
>   HEM360    CAC3   0.796
>   HEM360    FE43   0.557   0.557
>
> -------------------------------------------------------
> Program gmx pdb2gmx, VERSION 5.1.2
> Source code file: /home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, line: 645
>
> Fatal error:
> Residue 'HEM' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I added an entry in residuetype.dat (HEM      Protein), after making a copy in my working directory but it didn't fix the problem. I verified each file and they seem OK, I can't find where is the problem!!! Any help please!!!
>

The residue name is HEME, not HEM (specbond.dat changes it).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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