[gmx-users] pdb2gmx fails because of imaginary "Residue E"

[Justin Lemkul]

On 12/1/13 11:06 AM, kolnkempff wrote:
> Thanks Justin, I appreciate your patience with newbie questions.
>
> When I realign columns, I get:
> Fatal error:
> Atom H in residue ACE 1 was not found in rtp entry ACE with 6 atoms
> while sorting atoms.
>
> So I tried the flag -ignh which produced:
> Fatal error:
> Atom C in residue NME 3 was not found in rtp entry NME with 6 atoms
> while sorting atoms.
>
> So I manually edited the file to include all HC, CT, etc. labels (from
> aminoacids.rtp) which produced:
> WARNING: there were 6 atoms with zero occupancy and 23 atoms with
>           occupancy unequal to one (out of 32 atoms). Check your pdb file.
> ...
> Identified residue PHE0 as a starting terminus.
> Identified residue NME0 as a ending terminus.
> ...
> Fatal error:
> Atom CT in residue PHE 0 was not found in rtp entry NPHE with 22 atoms
> while sorting atoms.
>
> So it seems ACE has been lost.
>
> Any insight would be greatly appreciated.  Today, I'll try using amberTools
> to work with this.
>

It seems that whatever is in your input .pdb file is still badly mangled.  Using 
molecule editing software like AmberTools is a smart way to go rather than 
trying to haphazardly hack it yourself.  All of the above errors are either 
format or naming problems.

-Justin

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

Justin A. Lemkul, Ph.D.
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

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