[gmx-users] DT Fatal Error still remaining

[Justin Lemkul]

On 7/22/16 7:49 AM, Sanjay Singh wrote:
> I encountered a problem when I using pdb2gmx to convert a pdb file
> into gro and top file.by using  6: AMBER99SB-ILDN protein, nucleic
> AMBER94 Force field
>
> The system give me a fatal error message as following:Atom P in
> residue DT 501 was not found in rtp entry DT5 with 30 atoms while
> sorting atoms.
>
> Before above mention fatal error system give fatal error Residue 37
> named VAL of a molecule in the input file was mapped to an entry in
> the topology database, but the atom CG1 used in that entry is not
> found in the input file. Perhaps your atom and/or residue naming needs
> to be fixed .While valine naming is same in .rtp entry and pdb file
> this error is remove but DT 501 fatal error still remaining
>

AMBER uses special residue names for 5'-termini (D*5) and 3'-termini (D*3) so if 
your starting residue name is DT, pdb2gmx expects it to be an internal residue 
with a 5'-phosphate.  Rename the residues appropriately.

-Justin

-- 
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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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