[gmx-users] No .atp file could be found error in KALP-15 in DPPC tutorial

Justin Lemkul jalemkul at vt.edu
Fri Jul 18 17:40:59 CEST 2014

On 7/18/14, 11:34 AM, sjubaer at purdue.edu wrote:
> Hi,
> I am a new Gromacs user, and while I've been following the KALP-15 in DPPC
> tutorial, I seem to have hit a snag.
> 1. After the step where I manually edited the topology file and created the
> gromos53a6_lipid forcefield directory, I tried to convert the dppc128.pdb
> file to .gro format using pdb2gmx (Part 1 of Step 3). I used the
> gromos53a6_lipid forcefield when prompted, and used SCP. However, I received
> an error stating no ".atp" file could be found. None of the previous steps
> asked for the file, but I found and copied the file "atomtypes.atp" over from
> the original gromos53a6 directory and into gromos53a6_lipid.
> 2. This resolved the .atp file issue, but I received a second error stating
> "Residue DPP not found within residue topology database". I noticed some
> files reference the residue as DPPC instead of DPP, and maybe that might be
> the problem, but I am not sure what to change or where to proceed from here.
> Any help would be greatly appreciated!

At no point should you process the DPPC coordinate file with pdb2gmx.  The 
tutorial never calls for this, so you should not do it.  Conversion between .pdb 
and .gro format is done with editconf, as stated in the tutorial.  The purpose 
of pdb2gmx is to generate a topology; you already have the topology of DPPC, so 
you don't need to create a new one.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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