[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

[Dallas Warren]

This is an issue with CGenFF, nothing to do with GROMACS.

So you need to ask this question through the CGenFF help channel(s),
wherever that may be.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Wed, 21 Aug 2019 at 08:25, Maryam Sadat Sadeghi <
m_sadeghi at cmps2.iust.ac.ir> wrote:

> Hi All,
>
> I have created a crystal structure of 2 polymer chains (PEG) and I need to
> calculate the cohesive energy for my system using CHARMM36 FF. In this case
> my fix_mol2 file includes 2 ligands, to convert to str file I get the
> following error:
>
> readmol2 warning: non-unique atoms were renamed. Now processing molecule
> LIG ... attype warning: carbon radical, carbocation or carbanion not
> supported; skipped molecule.
>
> How can I fix this problem? Changing the ligand IDs and names does not
> help. I even tried to make 2 separate mol2 files for each chain in the
> crystal structure, but still get the same error while converting to str
> file...
>
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