Pradip Si

Thanks. It helped. I need one more suggestion. I am trying to run organic crystal simulation. Unlike gromacs gro file where atom names for each residue has to be same...

Yes, the same xml I copied here. It's a organic crystal so same molecule is repeating periodically. In gromacs run, your top file is for single molecule GAFF and at...

Thanks. It worked. For gromacs run previously, when I converted pdb to gro, even with same residue seq number it ran without any issue. Now I changed the residue seq...

One last thing, While printing the pdb file, the atoms name for the first three atom has changed, but the next run after Energy minimization, ran without any issue. I...

I have figured out the open babel issue. Bust still getting the error like, ``` /storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3307: SyntaxWarning: invalid escape sequence '\s' patt_list.append(('psi4', 'header', re.compile('^\s+Psi4\: An Open-Source Ab Initio Electronic Structure...

Hi, I am doing a poltype calculation for [this molecule](https://en.wikipedia.org/wiki/5-Methyl-2-((2-nitrophenyl)amino)-3-thiophenecarbonitrile). I am getting some errors which I couldn't understand much. ``` ============================== *** Open Babel Warning in ReadMolecule Failed to...

Hello, Thanks for the information. I have generated an XML file from the Poltype2 file using Force Field X. It gives me an error like ``` Traceback (most recent call...

The FFX FFtoXML tool doesn't consider the XYZ file to generate xml format. The order of the atoms is not similar and it's difficult to fix. I saw you generated...

Now the order is correct and it worked. For a "code" snippet you can try like (start and end with```).