[gmx-users] confirm please

Chetan Mahajan chetanvm10 at gmail.com
Tue May 13 01:32:25 CEST 2014

Dear All,

I am using amber2gromacs tool acpype for converting input files for AMBER
into those for GROMACS. There are some differences in these files (.gro and
.top) compared to the information given in gromacs manual 4.6.5 abotu these
kind of files.

First, while listing charges and vander waals parameters for all the atom
types in [atomtypes] directive, there is no second column titled as
"at.num" in the manual. Is that okay? What does that column mean anyways
(number of atoms of that type?)?

Second, where there is atom name and number to be mentioned for each atom
in a given molecule in .gro file,
numbering is not consecutively for all atoms as mentioned in the manual.
E.g. instead of OW1, HW1 and HW2 for water, it is just O, H1 and H2.
Instead of O1, O2 in formate, it's just O, O1.

>From my understanding, it seems okay, as long as atom name and number
(identity of that atom) is same in .gro as well as .top. However, I just
wanted to confirm it.

Thanks in advance!


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