[gmx-users] 2 questions: pdb2gmx and genbox

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jan 11 02:05:22 CET 2007


> 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?

If you use "man pdb2gmx" you will see the kind of usage you need to use. 
If you page down, you will see them all explained in detail.

If you look at the top of the output from pdb2gmx you will see the flags 
and values you actually passed on the command line reported back to you, 
together with any default values that you didn't override. "eiwit.pdb" 
is such a value, although I've no idea why a default structure file 
should be named that.

> 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?

If you've used genbox with the -p input (see "man genbox"), then you 
will have both filename.top and #filename.top.1# (the backup) and they 
will differ in the last few lines. Check with "diff filename.top 
#filename.top.1#" to do a line-by-line comparison.

Again, if you read the man pages (there's a theme here...) you will see 
that you can specify the name of the output structure file. Further, if 
you specify a name that includes a file extension of ".pdb" then that 
file will be a PDB file - no need for post-conversion. This is a general 
gromacs phenomenon.

You cannot "convert a .gro file to a .top file" since this is a 
non-trivial process, however pdb2gmx is the tool that comes closest to 
doing that. Any other tool might make modifications, but you need to 
start with a serious .top file and the ways to do that are to use 
pdb2gmx, do it by hand, or use the PRODRG server (for some systems).


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