James Starlight wrote:
Justin,
Could you tell me more about adding caps by amber tools?
1) I've found in that software ACE as well as other groups but they are
not standart
e.g ACE is below instead of simple CH3 group
ACE is an acetyl group, not a methyl. Those coordinates look fine.
949 HH31 ACE 29 2.000 1.000 -0.000 1.00 0.00
ATOM 950 CH3 ACE 29 2.000 2.090 0.000 1.00 0.00
ATOM 951 HH32 ACE 29 1.486 2.454 0.890 1.00 0.00
ATOM 952 HH33 ACE 29 1.486 2.454 -0.890 1.00 0.00
ATOM 953 C ACE 29 3.427 2.641 -0.000 1.00 0.00
ATOM 954 O ACE 29 4.391 1.877 -0.000 1.00 0.00
ATOM 955 H7 ACE 29 3.582 3.629 -0.000 1.00 0.00
have you edited that group to standart form in amber tools or used
something else ?
2) How you place CAP groups to desired coordinates?
E.g if I use Edit- Unit Import Unit I can just import desired groups to
my pdb coordinates but how make linckage with N and C termi of my
molecule ? Or that linkage would be build by pdb2gmx -ter option ?
You can draw them in xleap wherever you like. There's likely tutorial material
out there for such tings.
3) What another CAP groups in amber tools should I use for capping of
termi wich would be compatible with gromacs ff?
ACE and NH2 are built in to Gromos96; they will work fine.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
