[gmx-users] residue names in rtp file and their parameters

chiba.s.ac chiba.s.ac at m.titech.ac.jp
Mon Jul 5 00:59:24 CEST 2010

Dear gmx-users,

I am trying to derive parameters of novel molecules consistent with ffG53a6.  To get a feel of the parameterization, I am reading ffG53a6.rtp file.  Let me please ask some questions about ffG53a6.rtp.

My questions are as follows:
1) What molecules do residue names in rtp file stand for, respectively? Could you let me know the related literatures?
2) There are some residues which are not listed in the original paper of ffG53a5/6 (e.g. ATP, HEME). How were these parameters derived? Is it consistent with the method described in the paper, i.e. are charges fitted to reproduce the corresponding experimental value?

With respect to ffgmx.rtp, I found the correspondences between molecule full names and residue names at http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks .
However ffG53a6.rtp seems to have been updated in some respects.

Best regards,

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