Error due to line in input file longer than 4095 characters

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No

Hey guys!

I’m currently attempting to run a coarse-grained MD simulation on a large protein (>15000 residues) on Gromacs 2020.2, but I get the following error after minimization (attached below). There seems to be a few lines (one denoting the residue codes in order, and one denoting the secondary structure designations for all of them) that exceed 4095 lines, and I think they’re causing this error. Does anyone know how I can fix this?

I’ve seen other posts with the same issue in Gromacs 4.6.5, and some comments mention to edit the file “src/gromacs/gmxpreprocess/readir.cpp.” However, I couldn’t find this file in the Gromacs directory.

Thanks,
Surya

Program: gmx grompp, version 2020.2
Source file: src/gromacs/utility/cstringutil.cpp (line 97)

Fatal error:
An input file contains a line longer than 4095 characters, while the buffer
passed to fgets2 has size 4095. The line starts with: ‘; NKSQLYPDSPLTDQDFNQ’

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

2

What input files and which type of input them are causing the issues?

3

Hello,

It seems that the *.itp files that my *.top file is referencing have extremely long lines, due to the number of residues in my protein structure. The issue arises when I try to create a *.tpr file for minimization (before solvating the structure).

Thanks,
Surya

4

I don’t see how a line in the topology can get beyond 4095 characters because you have residue number requiring 5 digits. Could you post a problematic line?

5

Hello,
It seems that the long line in the *.itp file is there because Martini (which I’m using for coarse-graining) automatically adds a sequence and secondary structure codes for each residue at the beginning of the file:

; MARTINI (martini22) Coarse Grained topology file for “Protein_A”
; Created by py version 2.6
; Using the following options: -f enc_clean.pdb -o enc.top -x enc-cg.pdb -p backbone -ff martini22
; Sequence:

; NKSQLYPDSPLTDQDFNQLDQTVIEAA…

; Secondary Structure:

; CCCCCCCCCCCCCCCCCCCCCCCCC…

I guess this part of the file is not crucial for the run, so I think I’ll remove it for now, but then use it again when generating the trajectory files at the end, so that all atoms appear (and not just the backbone).

Thanks,
Surya