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

[sjubaer at purdue.edu]

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! 

Thanks, 

Shadman Jubaer 
Weldon School of Biomedical Engineering 
Purdue University Class of 2016