[gmx-users] How to overcome the error "Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom."

[Justin Lemkul]

On 11/3/14 12:32 AM, Seera Suryanarayana wrote:
> Dear gromacs users
>
> I have been tried to simulate the  protein-dna complex. I got error as
> "Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms
> while sorting atom" upon using the command pdb2gmx. I have been added the P
> atom and bonds of P in the .rtp file which is the part of AMBER99SB-ILDN
> force field. After the modification of the dna.rtp file I also got the same
> error which mentioned above.
> Kindly tell me how to overcome this error.
>

DNA does not normally have a 5'-PO4 cap, but apparently your structure does.  If 
it's some biologically interesting state, you'll need to add a .tdb entry to 
deal with having a phosphate group.  If not, delete the extraneous atoms.

-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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