# Pdb2gmx looking in wrong directory even though I changed GMXLIB

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-looking-in-wrong-directory-even-though-i-changed-gmxlib/3300>\
**Category:** User discussions\
**Tags:** pdb2gmx, simulation-setup\
**Created:** [December 13, 2021, 3:54pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-looking-in-wrong-directory-even-though-i-changed-gmxlib/3300 "2021-12-13T15:54:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![dkonstan](https://avatars.discourse-cdn.com/v4/letter/d/87869e/32.png) [@dkonstan](https://gromacs.bioexcel.eu/u/dkonstan)\
**Post date:** [December 13, 2021, 3:54pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-looking-in-wrong-directory-even-though-i-changed-gmxlib/3300/1 "2021-12-13T15:54:51Z")

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GROMACS version: 2016.5  
GROMACS modification: No

Hello!

I am trying to make a topology for N-methyl acetamide using GROMOS 53a6 ff. This force field doesn’t have an entry for NME (N-methyl capping group), but Tom Piggot from the GROMACS forum provided an rtp file. I put the rtp file in the same directory as the rest of the force field files (gromos53a6.ff) and copied it to my local directory. I then changed GMXLIB to the current working directory based on the pdb2gmx documentation. I now get this error:

**Feature not implemented:**  
**Can only select the first of multiple force field entries with directory name**  
**’gromos53a6.ff’ in the list. If you want to use the next entry, run pdb2gmx in**  
**a different directory, set GMXLIB to point to the desired force field first,**  
**and/or rename or move the force field directory present in the current working**  
**directory.**

As a side note, is having an rtp file enough to specify the topology for NME? If no, what else do I need and can anyone provide it? People in the literature have done simulations with NMA and this ff so it must be pretty straightforward (I think)…

Thank you!

Best,  
Dan

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [December 14, 2021, 8:24am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-looking-in-wrong-directory-even-though-i-changed-gmxlib/3300/2 "2021-12-14T08:24:13Z")

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Hi,  
I suggest to check GMXLIB setting of your shell. you can look at the environmental setting using the bash command ( \> env | grep ‘GMXLIB’ ).  
I think that pdb2gmx writes in standard output where is looking for forcefield file. This should be the case also for 2016, but I am not 100% sure.

I guess that you have added the rtp entry to rtp file. here you can find some information on how to add a residue [Adding a Residue to a Force Field — GROMACS 2021.4 documentation](https://manual.gromacs.org/current/how-to/topology.html?highlight=atom%20type)

Regards  
Alessandra