ram bio wrote:
Dear Justin,
Thanks and as per suggestion, now i have corrected the original
modelled pdb file and executed the pdb2gmx command with n-terminus
option 1 (NH2) and C-terminus option 1 (COOH), now the net charge is
11.00, and the toplogy file has the first and last residues as under:
1 NL 1 SER N 1 -0.66 14.0067
; qtot -0.66
2 H 1 SER H1 1 0.44 1.008
; qtot -0.22
3 H 1 SER H2 1 0.44 1.008
; qtot 0.22
4 CH1 1 SER CA 1 -0.22 13.019 ; qtot 0
5 CH2 1 SER CB 2 0.266 14.027
; qtot 0.266
6 OA 1 SER OG 2 -0.674 15.9994
; qtot -0.408
7 H 1 SER HG 2 0.408 1.008 ; qtot 0
8 C 1 SER C 3 0.45 12.011
; qtot 0.45
9 O 1 SER O 3 -0.45 15.9994 ; qtot 0
2950 N 285 PRO N 1280 0 14.0067 ; qtot 11
2951 CH1 285 PRO CA 1281 0 13.019 ; qtot 11
2952 CH2R 285 PRO CB 1281 0 14.027 ; qtot 11
2953 CH2R 285 PRO CG 1282 0 14.027 ; qtot 11
2954 CH2R 285 PRO CD 1282 0 14.027 ; qtot 11
2955 C 285 PRO C 1283 0.33 12.011
; qtot 11.33
2956 O 285 PRO OT 1283 -0.45 15.9994
; qtot 10.88
2957 OA 285 PRO O 1283 -0.288 15.9994
; qtot 10.59
2958 H 285 PRO HO 1283 0.408 1.008 ; qtot 11
Please suggest if it is ok, so that i can continue with the further steps.
No, that's your job as a scientist :) Besides, I can't necessarily say. Do
those protonation states model reality? Is your model a reasonable
representation of a true physical system? Does the net charge make sense? Your
original first residue was threonine, now it's serine. What exactly was your
"fix" to this problem?
These are the things that you should always consider. Only once you've solved
these issues can you proceed with any degree of confidence.
-Justin
Thanks,
Ram
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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/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/mailing_lists/users.php
