[gmx-users] pdb2gmx atom not found

[Justin Lemkul]

On 12/12/14 12:52 PM, xy21hb wrote:
> Dear all,
>
>
> I am introducing a residue named ABC into AMBER03 force field. I built up the aminoacids.rtp and aminoacids.hdb file,
> but when I pdb2gmx, it gives,
> "
> Atom HB1 not found in rtp database in residue ABC, it looks a bit like HB
> "
> I am pretty sure I use HB instead of HB1, and there is no atom called HB1 in any of the above-mentioned files.(including .pdb for pdb2gmx)
> then I changed my HB to HB1, it gives similar error,
>
>
> "
> Atom HB11 not found in rtp database in residue ABC, it looks a bit like HB1
> "
>
>
> It seems that pdb2gmx is appending the name with "1".
>
>
> Anyone knows why that is?
>

Probably due to the .hdb entry - if multiple H are to be built on a single heavy 
atom, numbers are appended so they have unique names.  But to take the guesswork 
out, you'll need to provide the exact text of the .rtp and .hdb files.

-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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