Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 597)
Fatal error:
Residue ‘DOP’ not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
First, did you read the link in the message?
Second, if you search the forum you will find related threads. The residue name (DOP in your case) is different from one case to another. E.g., the “Related Topics” below this one would be a good starting point for you.
hellow Magnusl
i am a new one user I have open the link but could not find the best answer if u have idea about if u share me I will be gladful. i am working on phospholipids and glycolipids . glycolipids can be read but here problem in dop which is phospholipids
The problem is that the force field does not recognize that phospolipid. The explanation is in Common errors when using GROMACS - GROMACS 2024.1 documentation.
As I said, the related topics, below your post, is also useful, such as: Fatal error: Residue 'EDO' not found in residue topology database - #4 by jalemkul and Fatal error: Residue "NAG' not found in residue topology database.
I read but did not solve