On Fri, Mar 22, 2013 at 2:36 PM, Anna MARABOTTI <amarabo...@unisa.it> wrote:
> > 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). > OK, that's doubly good news. 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... > You'll have to start with the Antechamber documentation to find out the use of and dimensions for those numbers. I have no idea at all, but I'd not be surprised to hear that it was kcal mol-1 A-2 and perhaps a stray factor of 2 missing from the equation in which it works. That would account for the factor of ~800 you see here. You have the option of editing ffbonded.itp (so the lookup from [bonds] is done via the two atom numbers, which index into [atoms] to get the two atom names, which index into [bondedtypes]) or on the relevant line of [bonds] (just dumping the same function type and parameters you'd use in ffbonded.itp). What to do depends how much you plan to re-use the output of Antechamber. Mark > 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 > -- 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
