Error on trjconv -fit rot+trans

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1

GROMACS version: 2020.1
GROMACS modification: Yes/No
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Hello!

I’m trying to run gmx trjconv using this line command:

gmx trjconv -s nw.tpr -f nw.gro -o nw.gro -fit rot+trans

And I found this:

Program: gmx trjconv, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/fileio/groio.cpp (line 148)

Fatal error:
Invalid line in Protein in water t=150660.0000 step= 75330000 for atom 212: 23 ASN

For more information and tips for troubleshooting, please check the GROMACS website at: Common Errors — GROMACS webpage https://www.gromacs.org documentation

Can you help me to solve this?

2

Hello!

It looks like your GRO file is truncated or otherwise damaged. Specifically, there’s a line “23 ASN”, without any coordinates.

3

Do you know how can I solve it?

I’d fixed it pbc before, using:

gmx trjconv -s nw.tpr -f nw.xtc -o nw.gro -pbc mol -center

And nothing seemed to be wrong. What can I do?