Hi everybody, I'm trying to build a biotinilated peptide, i found some biotin parameterization but when I tried to build the peptide i found some problems and i think that my problems are related to the parameters. Do you have some advices about it? thank you in advance
It seems that the RTF and PARAmeter files you have are incomplete wrt biotin (or possibly not used in the correct way); you could check with the person/group that provided the files. Or you add the missing parameters to the parameter file - this could be straightforward if parameters for similar groups are already available.
Lennart Nilsson Karolinska Institutet Stockholm, Sweden
Here I am again, sorry if I look like too intrusive, so I follow your advice Prof. Lennart, and I generated a pdb, unfortunately the coordinates for the btn residue still non defined and i don't understand why to link the two segments i modified PRES LINk (as it possible to see down here. (i used this patch because the link that the biotin form with the residue is similar to a peptidic link, i've just changed the name of the atoms) thank you again
PRES LINK 0.00 ! linkage for IMAGES or for joining segments ! 1 refers to previous (N terminal) ! 2 refers to next (C terminal) ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C1 2N IMPR 2N 1C1 2CA 2HN 1C1 1C10 2N 1O1 IC 1O1 1C10 1C1 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1C10 *1C1 1O1 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C10 1C1 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C1 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C1 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000