GROMACS version: 2022.4
GROMACS modification: Yes/No no
Here post your question
I want to generate a OPLS FF of a polymer(30mer) using ACPYPE, but I get an error saying that the maximum bond limit (512 bonds) has been exceeded.
Does exceeding the max bond limit prevent the calculation?
Is there any workaround to solve this issue?
==========================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2025 AWSdS |
DEBUG: CLI: -i pnipam_30mer.mol2 -s 86400 -d
DEBUG: Python Version 3.11.6 | packaged by conda-forge | (main, Oct 3 2023, 10:40:35) [GCC 12.3.0]
DEBUG: Max execution time tolerance is 1d
DEBUG: /opt/anaconda3/envs/acpype/bin/antechamber -dr no -i pnipam_30mer.mol2 -fi mol2 -o tmp -fo ac -pf y
DEBUG:
Welcome to antechamber 22.0: molecular input file processor.
Info: The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
Info: The number of bonds (512) exceeded MAXBOND.
Warning: The assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
(be cautious, using a large value of PSCUTOFF (>100) will
significantly increase the computation time).
Info: The number of bonds (512) exceeded MAXBOND.
Thank you in advance.