Hi,
In order to make an amidated c-terminal, I used CT2 in charmm ff at the c-terminal. The last residue of my peptide is serine, and the total charge of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the c-terminal, and then getting top file, when I see the top file, everything is ok up to the amidated serine residue. But something wrong is with the charged amidated serine; the total charge is not equal to 5.00 : . . . 361 C 22 LYS C 361 0.51 12.011 ; qtot 5.51 362 O 22 LYS O 362 -0.51 15.999 ; qtot 5 ; residue 23 SER rtp SER q -0.0 363 NH1 23 SER N 363 -0.47 14.007 ; qtot 4.53 364 H 23 SER HN 364 0.31 1.008 ; qtot 4.84 365 CT1 23 SER CA 365 0.07 12.011 ; qtot 4.91 366 HB 23 SER HA 366 0.09 1.008 ; qtot 5 367 CT2 23 SER CB 367 0.05 12.011 ; qtot 5.05 368 HA 23 SER HB1 368 0.09 1.008 ; qtot 5.14 369 HA 23 SER HB2 369 0.09 1.008 ; qtot 5.23 370 OH1 23 SER OG 370 -0.66 15.999 ; qtot 4.57 371 H 23 SER HG1 371 0.43 1.008 ; qtot 5 372 C 23 SER C 372 0.51 12.011 ; qtot 5.51 373 NH2 23 SER NT 373 -0.62 14.007 ; qtot 4.89 374 H 23 SER HT1 374 0.3 1.008 ; qtot 5.19 375 H 23 SER HT2 375 0.32 1.008 ; qtot 5.51 376 O 23 SER O 376 -0.55 15.999 ; qtot 4.96 I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last residue is positive charged? Do the defined atom charges are supposed to be modified in last residue ? Would you please give me suggestions? Thanks in advance. Sincerely, Shima -- 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
