[gmx-users] Simulation queries

[Justin Lemkul]

On 3/14/17 9:04 AM, Acqualine Lobo wrote:
> Thanks!
>
> I did try replacing HEM with HEME without shifting the columns. This time I
> get an error for the missing H atoms and several warnings.
>
> ------------------------------------------------
> WARNING: atom HA is missing in residue HEME 137 in the pdb file
>          You might need to add atom HA to the hydrogen database of building
> bloc
>                                       k HEME
>          in the file merged.hdb (see the manual)
>
>
> WARNING: atom HB is missing in residue HEME 137 in the pdb file
>          You might need to add atom HB to the hydrogen database of building
> bloc
>                                       k HEME
>          in the file merged.hdb (see the manual)
>
>
> WARNING: atom HC is missing in residue HEME 137 in the pdb file
>          You might need to add atom HC to the hydrogen database of building
> bloc
>                                       k HEME
>          in the file merged.hdb (see the manual)
>
> etc etc..
>
> Fatal error:
> There were 30 missing atoms in molecule Other_chain_A2, 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
>
> ------------------------------------------------
>
> I did use the -ignh option with pdb2gmx, still I get this error!
>

Because this is not what -ignh does.  The -ignh tells pdb2gmx to ignore H atoms 
in the input coordinate file, especially useful in the case of non-standard 
naming.  That doesn't cause it to magically build H atoms back.  You will need 
to do one of two things, either (1) build H atoms on to the heme structure in a 
manner that conforms to CHARMM nomenclature, e.g. using CHARMM or CHARMM-GUI or 
(2) write an .hdb entry that tells pdb2gmx how to build H atoms onto heme.

-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

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