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

Allen Smith easmith at beatrice.rutgers.edu
Thu Oct 4 02:59:23 CEST 2007

In message <mid+200710032309.l93N9sL21343576 at dogberry.rutgers.edu> (on 3
October 2007 19:09:54 -0400), easmith at beatrice.rutgers.edu (Allen Smith)
>In message <4703D995.40608 at anu.edu.au> (on 4 October 2007 04:04:05 +1000),
>Mark.Abraham at anu.edu.au (Mark Abraham) wrote:
>>Allen Smith wrote:
>>> 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 :-)
>However, in this case, the original poster has not only edited down the
>solvent, but the bilayer. I am reasonably certain that if I put in more than
>one copy of something which is in a .rtp file and _not_ in, say, ions.itp,
>then it will be in both times in the .top file (after all, two
>different-position glycines are in twice in the .top file...).

Correction: multiple copies of an ion present in the .pdb file input into
pdb2gmx come out multiple times in the .top file (even though the ion is in
ions.itp), at least for a case in which they're not distinguished by chain
id from the rest.


Allen Smith			http://cesario.rutgers.edu/easmith/
September 11, 2001		A Day That Shall Live In Infamy II
"They that can give up essential liberty to obtain a little temporary
safety deserve neither liberty nor safety." - Benjamin Franklin

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