Hi folks, I have a problem with a "strange" residue into a PDB file. It is a cysteinesulfonic acid, in which the -SH moiety of the Cys residue is replaced by -SO3. This modified residue is essential for the activity of this protein, therefore I must keep it into the protein. So, I'm trying to add this new residue to the force field (I'm planning to use the 43a1ff already modified for lipids in the past). Since I have Gromacs 4.5.3 I copied the ff directory on my local dir, then I attempted to modify the aminoacids.rtp file and other files following instructions in the section "Adding a residue to a force field". In order to have some hints on OCS topology, I used PRODRG, at least to have some indication on atom, bonds and angle types, but in the .itp file obtained from PRODRG there are several data for which I don't find the corresponding element in the ffbonded.itp file. For example, I don't see any equivalent for the CB - SG - OD1 angle. Probably I should add them to the ffbonded.itp file, but I'm unsure how to do it. Is there an order to follow, or can I simply add a new element at the end of the [ angle ] section? Can anyone give me some hint to do it correctly, and more generally to manage correctly the whole problem? Thanks a lot Anna Marabotti __________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano)
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