[gmx-users] 2 questions: pdb2gmx and genbox

WILLIAM R WELCH wwelch at wisc.edu
Thu Jan 11 00:16:27 CET 2007

Hello, I am a brand new gromacs user--I have been banging my head against the wall with the manual for some time, so if someone could be so gracious, I have 2 simple questions:

In the tutorial files I obtained in gromacs 3.3, on if I use pdb2gmx with no file specified, I get the input/output error an with the words "eiwit.pdb"  So if I specify a pdb file, I get the error " invalid argument".  What am I supposed to type on the command line to get this file to convert?

Also, I used editconf and genbox to solvate a peptide chain in the tutorial "nmr1".   I got an output file with all of the waters added called out.gro as expected, but I need a .top file with the waters in it to use grompp--It seems to me that the topol.top file has not changed one bit (no waters added) by using genbox, although the demo clearly states that this should happen. How can I convert the .gro file to a topology file and can I also get a pdb file back out?

Will Welch

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