[gmx-users] DPPC hlothane Residue DPP not found in residue topology database
jalemkul at vt.edu
Mon Nov 9 19:14:06 CET 2015
On 11/9/15 1:11 PM, Poncho Arvayo Zatarain wrote:
> Hello: Concerning about my last question of DPPC membrane and halothane simulation and the GROMOS 53a6. When i used pdb2gmx the following error appears: Residue DPP not found in residue topology database. Then, i googled to Gromacs webpage and i found XXX'_not_found_in_residue_topology_database. So, after that and because a suggestion that probably GROMOS53a6 is not the best stock for simulate membranes, i tried every option of forcefield that GROMACS presented to me: Amber93 protein Amber94 nucleic, Amber94 forcefield, Amber96 protein nucleic Amber94, Amber99 protein nucleic Amber94, Amber99SB Protein, nucleic Amber 94, AmberGS forcefield, CHARMM27 all-atom forcefield, Gromos96 43a1, 43a2, 45a3, 53a5, 53a6, 54a7 and OPLS-AA/L and the same error appears in every orcefield: Residue DPP not found in residue topology database. What can i do? Because i simulated an Apoferritin-halothane and DPPC membrane with water and used GROMOS5a6 and everything was fine, but not this time.
Lipid residue names are 4 characters in most (all) force fields. So your
problem is very self-explanatory: it's wrong and needs to be changed to match
the force field (whichever one you choose).
$ grep "DPP" *.ff/*.rtp
charmm36.ff/merged.rtp:[ DPPA ]
charmm36.ff/merged.rtp:[ DPPC ]
charmm36.ff/merged.rtp:[ DPPE ]
charmm36.ff/merged.rtp:[ DPPG ]
charmm36.ff/merged.rtp:[ DPPS ]
gromos43a1.ff/aminoacids.rtp:[ NDPP ]
gromos43a2.ff/aminoacids.rtp:[ NDPP ]
gromos45a3.ff/aminoacids.rtp:[ NDPP ]
gromos53a5.ff/aminoacids.rtp:[ NDPP ]
gromos53a5.ff/aminoacids.rtp:[ DPPC ]
gromos53a6.ff/aminoacids.rtp:[ NDPP ]
gromos53a6.ff/aminoacids.rtp:[ DPPC ]
gromos53a6_lipid.ff/aminoacids.rtp:[ NDPP ]
gromos53a6_lipid.ff/aminoacids.rtp:[ DPPC ]
gromos54a7.ff/aminoacids.rtp:[ NDPP ]
gromos54a7.ff/aminoacids.rtp:[ DPPC ]
Note that none of them say "DPP."
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
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