[gmx-users] dna with charmm36

[Justin Lemkul]

On 3/3/14, 7:57 PM, gromacs query wrote:
> Hi All
>
> Its in continuation. I am confused about something. In PDB file obtained
> from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them.
> PDB has DC5 as starting and DT3 as end residue and I get this error:
>
> pdb2gmx -ter -ff charmm36-jan2014 -f test.pdb -o test.gro ( with or without
> -ignh)
>
> WARNING: atom H3' is missing in residue DC5 1 in the pdb file
>
>           You might need to add atom H3' to the hydrogen database of
> building block DC5
>
>           in the file merged.hdb (see the manual)
>
>
>
> WARNING: atom H5'1 is missing in residue DT3 10 in the pdb file
>
>           You might need to add atom H5'1 to the hydrogen database of
> building block DT3
>
>           in the file merged.hdb (see the manual)
>
>
>
> I found DC5 and others (D*5 and D*3) are missing in merged.hdb. Are these
> missing or intentionally not added? Also if I change name of DC5 to DC and
> DT3 to DT it works fine and all Hs are added without error.
>

Specific naming of terminal residues like this is not needed for CHARMM.  Just 
choose the correct termini (5TER and 3TER) and they will be patched appropriately.

-Justin

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

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

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