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

Allen Smith easmith at beatrice.rutgers.edu
Wed Oct 3 19:49:39 CEST 2007

In message <9024f1330710031013t10772b86nfb62129ec625c03e at mail.gmail.com> (on
3 October 2007 19:13:51 +0200), mariagoranovic at gmail.com (maria goranovic)
>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.

>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.

>My goal is now to obtain a proper input to the
>grompp program, which is a good .gro and a .top file. The latter I already
>pdb2gmx is not working for me with the error:
>%Fatal error:
>%Residue 'DPP' not found in residue topology database
>Q1. How do I add my topology file to the database ?

What is DPP? Perhaps it's under another name in the original .top and .gro
files, in which case you should change the name in the .pdb file input to
that name?

>Q2. The second question is regarding the use of genbox and editconf. How can
>I specify the box size such that no more solvent is added to the system ?
>Using the following two options adds more solvent to the system, which I do
>not really need
>% editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90
>-bt triclinic -o input.gro -c -center 0 0 0

I tend to use -princ, to align the longest axis of the input with the
longest axis of the box (17.3 in your case). Not sure if that would be
advisable with a bilayer system, however.

>% genbox -cp input.gro -o output.gro -cs spc216.gro
>I chose the box size based on the maximum and minimum coordinates of the
>heavy atoms of the system.

Do heavy atoms include the oxygens in the waters? If so, then I would think
that that should be an adequate size (I trust you allowed for gromacs using
nanometers while PDB files use angstroms?); I would suspect things would be
too crowded otherwise. However, if you use -princ, you will probably need to
check to see exactly what dimensions it comes out to have prior to putting
it into the box, since it may align it differently than it is already

>Does one have to do the above procedure by
>iteratively changing the box size until genbox adds no more solvent ?

If you don't want more solvent added, don't use genbox. The question will be
how to do this while making sure you don't have any vacuum spaces.


Allen Smith			         http://cesario.rutgers.edu/easmith/
There is only one sound argument for democracy, and that is the argument
that it is a crime for any man to hold himself out as better than other men,
and, above all, a most heinous offense for him to prove it. - H. L. Mencken

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