You forgot to pass topol.top to solvate -p, so it didn't get updated with the addition of water. Check out some tutorials here: http://www.mdtutorials.com/gmx/

The flowchart on the GROMACS site is only a bare-bones piece of information. I also strongly recommend not using outdated software. Use version 2018.2 for all the latest feature upgrades and bug fixes. 5.0.7 is quite old at this point.

You forgot to pass topol.top to solvate -p, so it didn't get updated with the addition of water. Check out some tutorials here: http://www.mdtutorials.com/gmx/

The flowchart on the GROMACS site is only a bare-bones piece of information. I also strongly recommend not using outdated software. Use version 2018.2 for all the latest feature upgrades and bug fixes. 5.0.7 is quite old at this point.

Hi Justin,

Thanks you very much for your prompt response. The given manual worked for me in case of protein only while I am following it for protein-ligand complex it terminates with below error -

[vkc@localhost 2_MDS]$ python cgenff_charmm2gmx.py lig 28.50_fix.mol2 28.50.str charmm36-jul2017.ff

Traceback (most recent call last):

File "cgenff_charmm2gmx.py", line 47, in

import networkx as nx

ImportError: No module named networkx

In addition to this i tried to install Avogadro program it don't installed, it ask for openbabel and which is already installed openbabel-2-4-1. However, I already have mol2 files of ligands and excuted below command

perl sort_mol2_bonds.pl -28.50.mol2 28.50_fix.mol2 completed without error. After this I executed cgenff_charmm2gmx.py which failed with above error.

Please help.

Gopal

You need to install the NetworkX Python package. Please heed the tutorial's warning about the necessary version of this package.

I also had a similar problem with the new update of GROMACS tutorial. With the latest python package i could not obtain ligand topology fixed file. Also, with python 2.7 version NetworkX didn't install because of some other requirements (I forgot what package).

When number of coordinates does not match with that in topology file there is a way to pass it through, of cause i do not now if it is right to do. As i remember you may subtract14627 and 2177 which makes 12450 (12450/3=4150) and further deduce 4150 from the value in the last line (SOL) in the topology file.

There is also an other way, in which one can divide 14627 to 2177 (6.719) and then divide the SOL value in the topology file by 6.719. Re-running the GROMACS command may still show you some other differences (but close values) in both coordinates that you are able to perform such process again to meet the desired result.