Generate a file containing atom charges informations. (like .pqr)

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hello,

I am doing simulations of a protein nanopore-membrane system, and would like to create electrostatic potential maps using VMD pmepot plugin. For this, I need a topology file containing atom charges informations, often a .pqr file. I tried to generate it using -grasp command of gmx trjconv, but the results are wrong (huge inconsistent) values and after discussions with members of the lab I am doing this project in, they told me that they had the same issue and used NAMD to create these (charges informations are stored directly is the topology file). However, I want to stick with gromacs since all my simulations are already done! Is there a way where I can get such file using gromacs? After searching over the internet, I could not find a right way to do it!

Best,
Thomas Castiglione

2

Does anyone have an idea? Sorry to push, but my work is due soon ^^.

3

VMD is generally more suited to dealing with CHARMM-style file formats, which is why you can use PSF to really easily populate charges into a coordinate file. GROMACS topologies can, in principle, give you the same information but it may be more cryptic via the use of #include statements. I’d suggest using gmx dump to print out a full topology with all charges, then write a script to simple add these to your PDB file to make a PQR.

4

All right thank you very much for your help, I’ll try this!