On Mon, May 14, 2012 at 1:51 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 14/05/2012 10:42 PM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> i run the implicit simulation with virtual sites on the hydrogen of my >> protein. Now I want to extract coordinates and run another simulation (in >> explicit solvent). Is there any way to remove those virtual sites from my >> gro file as VMD write the file using atoms not recognized by pdb2gmx >> obviously? Please, help! >> > > If your original pdb2gmx workflow with virtual sites was recorded in a > shell script you'd > a) have a record for when you go to write up, and > b) be able to do this change easily. > > As it is, a few minutes with a text editor would probably work for small > systems. Alternatively > > grep -v MCH3 in.gro > temp.gro > > will remove all of the lines for virtual sites named MCH3. Do that for > each type of virtual site. Adjust the count of atoms at the top of the .gro > file suitably at the end. > > Mark Thank you Mark! Steven > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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