[gmx-users] partial charges, editconf -grasp

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 3 16:35:22 CET 2008

Una Bjarnadottir wrote:
> Dear Gromacs users,
> I want to extract partial charges from a trajectory file. I know only of
> using trjconv to write individual frames to individual files and then using
> editconf with the grasp option on each of these files. But when I do:
> editconf -f xxx.gro -o xxx.pdb -grasp
> I get the following error:
> Fatal error:
> Input file should be a .tp[abr] file when using the -mead option.
> I thought this was a version 3.3.x problem after reading "Editconf fix" on
> http://www.gromacs.org/pipermail/gmx-revision/2008-February/000202.html. 
> But
> I just upgraded to version 4.0 and I get the exact same error. Can anyone
> help me with this problem? Is there perhaps an easier way of getting the
> partial charges?

Have you done what editconf is telling you?  Charges are not stored in 
coordinate files by default, so there are no charges to read.  Charges are, 
however, in the topology (.top), which is then passed to the .tpr file.  If you 
supply the .tpr, it should work.


> Kind regards,
> Una


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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