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

Chris de Graaf degraaf at chem.vu.nl
Fri Aug 23 14:08:08 CEST 2002

Chris de Graaf wrote:

> 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

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 Dear gmx users,

Meanwhile I seem to have found a solution to the problem described above,
although I must admit that it isn't a very elegant one. I replaced the H
atoms I want to "keep" in my topology file by C atoms within INSIGHT2 and
saved this structure as a pdb file. Although the original atom numbering is
maintained, I subsequently changed the atom names in this pdb file (H1=C15,
H2=C16, etc.) and deposited this file at the PRODRG server. In this way, a
structure is generated with CH3 groups instead of H atoms conected to the
aromatic rings. By looking at the image provided by PRODRG, one can again
change the atom names of these C atoms into H atoms in the PRODRG pdb file,
and do the same for the GROMACS topology file (the nice thing is that for
the definition of force field parameters in this topology file atom numbers
(consistent with the atom sequence in the PRODRG pdb file) are used instead
of atom names).

However, as I sead earlier, this is not a very elegant solution, so other
suggestions are very welcome.

thanks in advance and with kind regards,

Chris de Graaf

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