[gmx-users] getting a good .gro file from a pdb file while the topology is ready

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 3 20:04:05 CEST 2007

Allen Smith wrote:
> In message <9024f1330710031013t10772b86nfb62129ec625c03e at mail.gmail.com> (on
> 3 October 2007 19:13:51 +0200), mariagoranovic at gmail.com (maria goranovic)
> wrote:
>> Hi,
>> I had a large bilayer in .gro and .top gromacs format files
> Bilayer? I believe there are some specific things for doing planar periodic
> boundary conditions (or planar infinite system conditions), but I am not
> familiar with them.

Yeah but they're in the .mdp and not the issue here :-)

>> which I truncated to make a smaller bilayer, and added some more water
>> molecules, using programs other than gromacs. The final output I have is a
>> pdb file with complete solvation, and a topology file which I obtained from
>> the original top file by simply changing the number of residues of each
>> group in the last section.
> Umm... the atom numbers (not just the numbers of residues) are going to need
> to correspond between the .top and .gro files.

I think the OP meant changing the number of molecules in the [molecules] 
section of the .top file. I expect that within each molecule in the 
structure file the order of the atoms must agree between with the 
topology file. Certainly the order of the molecules in the [molecules] 
section must correspond to that in the structure file.

However, the atom numbers cannot (in general), match in order between 
structure and topology file for any system with more than one copy of a 
molecule (e.g. solvent). For simple solvated systems where one gets 
focussed on the solute, it can look like correspondence is occurring and 
thus might be necessary :-)


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