Dear gmx-users,
I'm still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it as a new residue. I'm trying (VERY hardly) to add missing parameters into ffbonded.itp file for AMBER99SB ff, using those parameters found in files calculated by Antechamber. To date, I've added those parameters related to bonds, now I have to add those related to angles, dihedrals and impropers. I'm dealing with section [angletypes] of file ffbonded.itp, and I'm looking at the values of cth (that I imagine is the angle force constant expressed in kJ mol^-1 rad^-2, correct?) I see that all parameters in ffbonded.itp are multiple of the value of 4.184, corresponding to the conversion factor between kcal and kJ. If I divide each of these values, I obtain a value corresponding to a number such as 80, 70, 120, 40 etc. Instead, if I look at those corresponding values found using Antechamber, I see, as expected, numbers with decimals, that are often very different from those present in ffbonded.itp (when I compare angles present in both files). For example, for the angle CT-CT-CT (3 C sp3), I see in ffbonded.itp a value of cth equal to 334.72 kJ mol^-1 rad^-2. For the same angle, Antechamber calculated a value of 63.21 kcal/mol^-1 rad^-2. If I do 334.72/4.184 the result is 80, which is different from the value of Antechamber. If I consider the angle CT-CT-HC (2 C sp3 and one H) the angle force constant in Antechamber is 46.37 kcal mol-1 rad-2, in ffbonded.itp is 418.4, that divided by 4.184 is exactly 100. Moreover, the same values of angles and forces are applied to angles that in my opinion are quite different among them. For example, I found the same value of 109.5 (th) and 418.4 (cth) for: H2-CT-N*, H1-CT-N*, H1-CT-OH, H1-CT-OS, H2-CT-OS, N*-CT-OS, C-CT-H1, H1-CT-N2, C-CT-HC... All these angles involve atoms that seem very different to me, and I'd expect to find different values of these parameters. It seems to me that values into ffbonded.itp related to these force constants are quite "strange", especially for the fact that they are EXACTLY multiple of 4.184, and I wonder if I'm correctly interpreting these values. Best regards Anna -- 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
