[gmx-users] No default U-B types in CHARMM36 FF

[Justin Lemkul]

On 4/13/14, 1:32 PM, Albert wrote:
> IC.
>
> I run it again, and select all the options as none. However, it claimed that
> hydrogens in NMA is missing. shouldn't pdb2gmx add hydrogens to residues
> automatically?
>

pdb2gmx doesn't do anything by magic.  As with any residue, H atoms will only be 
added if there is an .hdb entry for it.

-Justin

> End terminus NMA-339: None
> Opening force field file
> /soft/gromacs-4.6.5/share/gromacs/top/charmm36-mar2014.ff/merged.arn
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 305 residues with 4847 atoms
> Making bonds...
>
> WARNING: atom H is missing in residue NMA 339 in the pdb file
>           You might need to add atom H to the hydrogen database of building
> block NMA
>           in the file merged.hdb (see the manual)
>
>
> WARNING: atom HH31 is missing in residue NMA 339 in the pdb file
>           You might need to add atom HH31 to the hydrogen database of building
> block NMA
>           in the file merged.hdb (see the manual)
>
>
> WARNING: atom HH32 is missing in residue NMA 339 in the pdb file
>           You might need to add atom HH32 to the hydrogen database of building
> block NMA
>           in the file merged.hdb (see the manual)
>
>
> WARNING: atom HH33 is missing in residue NMA 339 in the pdb file
>           You might need to add atom HH33 to the hydrogen database of building
> block NMA
>           in the file merged.hdb (see the manual)
>
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.5
> Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2top.c, line: 1588
>
> Fatal error:
> There were 4 missing atoms in molecule Protein_chain_X, 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
> -------------------------------------------------------
>
> "One Cross Each" (Monty Python)
>
>
>
> On 04/13/2014 07:17 PM, Justin Lemkul wrote:
>> Your ending terminus should be None, not 3TER.  3TER is for nucleic acids.
>

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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