Following Gromacs Manual and other suggestions from different topics I create a molecule with Avogadro, I decided to employ oplsaa ff (I copied it in a local directory giving a new name) and I manipulated $.rtp and atotype file, even updating residuetypes.dat.
Running gmx with the following command : gmx pdb2gmx -ff oplsaa_01 -f $.pdb the following message appears....
Program: gmx pdb2gmx, version 2018.1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639)
Fatal error:
Residue 'EC' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
any suggestion?
Hi Simone! It all depends on how you were "manipulating" your files. When you copied the folder of oplsaa.ff in the folder from which you were going to create the files you should be naming it exactly as forcefield.ff. In rtp-file of your forcefield you shall have the same residue. The last thing to check then is your PDB-file: how you name your residue there. You shall consider that if symbols with the residue name moved or if they do not have the same name you might get this error.
After making all changes then you would be able to run the following in the terminal:
gmx pdb2gmx -f yourfile.pdb -o yourfile.gro
Then select 1 as your forcefield.
Inna Ermilova seem to be incredible, but I found the error re-writing the pdb and aminoacids.rtp files. The problem it simply a "bar problems" related to the spaces you leave among columns writing your files. I faced the same problem with other tests and studies I did these days. Thank you anyway for your precious answer. Now I'm doing an hexabenzocoronene simulations and everything seems to be ok.
Hi Simone
be sure that you copied the oplsaa ff in src/....
be care about the place it is in the root place (sudo so command|)
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