Dear Mark, Justin and other gmx-users, thank you very much for your help. Thanks to your suggestions, I made some steps forward, but still I don't see the end of my travel...
First of all, I would like to say that my previous problem was solved when I renamed O1 to OA. Justin was right. When I did it, no other error messages came from pdb2gmx (including the "long bond" warning). Now...let's go to the following problem... :'( After pdb2gmx, editconf, genbox, here I am with grompp... When I made it, the fatal error was a list of No default Bond types No default angle types No default Proper Dih. types No default Improper Dih. types all referred to CFY, obviously. I know what the problem is, I don't know how to solve it. I did not add bonded types to ffbonded.itp because I was sure they all were present. Instead, there are some bonds that are not present. I have the parameters calculated for these bonds by Antechamber suite, but I don't know how to convert their format to the format required by ffbonded.itp. For example, this is the entry I have for a CT-CT bond in the output coming from Antechamber: CT-CT 303.10 1.535 same as c3-c3 and this is the entry for a CT-CT bond in ffbonded.itp: CT CT 1 0.15260 259408.0 ; 7,(1986),230; AA, SUGARS I can imagine that 1.535 and 0.15260 is the bond length (in A in the first case, in nm in the second case) and they are more or less identical. But how can I obtain the second value in ffbond.itp (the kb in kJ mol-1 nm-2) from the data I have? I don't recognize at all the value... I know that this is not strictly referred to Gromacs, anyway could you please tell me at least how can I find information on how to add these parameters properly? Anna ______________________________________________ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 "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) Il 21/03/2013 21:53, gmx-users-requ...@gromacs.org [1] ha scritto: Links: ------ [1] mailto:gmx-users-requ...@gromacs.org -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
