[gmx-users] generate GROMACS topology files using the PRODRG server

[Chris de Graaf]

Dear gmx-users,

I have been trying to use the PRODRG server to generate GROMACS topology
files for some organic molecules using the PRODRG server. An example of
one of these molecules is diclofenac, containing two aromatic rings
connected via a nitrogen atom:


        H3         H4
           C4--C5
          /            \
 H2-C3           C6-H5
          \             /                          H6
            C2--C1      Cl1-C8--C9
            /           \             /             \
   H9C13H10   N1---C7            C10-H7
        /                H1          \             /
O1-C14-O2           Cl2-C12--C11
                                                    H8


Within GROMACS, I want to use the GROMOS96 43a1 force field. The PRODRG
server however, automatically deletes all hydrogens and only (re)creates
"polar" hydrogens (in  this case only the H1 atom (conected to nitrogen)
and not the H atoms conected to the aromatic C atoms), when generating a
GROMACS topology file. However, I also want to "keep" the H atoms
conected to the aromatic carbons (such as is the case for, for example,
phenylalanine) in the topology file. To solve this problem, I changed
these H atoms in I or C atoms (keeping the numbering consistent), but in
these cases the PRODRG server gives the error that C2 is connected to 5
atoms (C1, C3, C13, H9 (I9) and H10 (I10), although these hydrogens are
conected to C13). This also happens when I add a "CONECT" section
(generated with babel) to the pdb file. Has anyone else also encountered
these problems and/or are there ways to overcome these problems?

thanks in advance and with kind regards,

Chris de Graaf