# Pdb2gmx takes x10 more time when run on gro rather than pdb. WHY?

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-takes-x10-more-time-when-run-on-gro-rather-than-pdb-why/1827>\
**Category:** User discussions\
**Tags:** pdb2gmx, forcefield\
**Created:** [March 25, 2021, 4:10pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-takes-x10-more-time-when-run-on-gro-rather-than-pdb-why/1827 "2021-03-25T16:10:48Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![sunidhi17148](https://avatars.discourse-cdn.com/v4/letter/s/439d5e/32.png) [@sunidhi17148](https://gromacs.bioexcel.eu/u/sunidhi17148)\
**Post date:** [March 25, 2021, 4:10pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-takes-x10-more-time-when-run-on-gro-rather-than-pdb-why/1827/1 "2021-03-25T16:10:48Z")

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GROMACS version: 2020.1  
GROMACS modification: No

I am working with a structure which when run via pdb2gmx to create a topology file, has a **mass of 71794** and only **27071 dihedrals**. When I convert the same PDB to a gro file (via editconf) and then run pdb2gmx with this gro file, the numbers increase drastically: **1050483.282 mass and 396893 dihedrals**. Why is this happening?

PDB file creates some issues like throwing this error- " _The residues in the chain ARG178–ATP1003 do not have a consistent type. The first residue has type ‘Protein’, while residue ATP1001 is of type ‘Other’. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory_ ." and **then crashes**. For getting rid of this error, I converted the PDB to a gro and started pdb2gmx. When it didn’t complete even in 4 hours (with PDB it takes only 10 minutes), I cross-checked and came across the mass and charge and dihedrals (all stats increased) issue. Why is this happening? Please guide me through this.