[gmx-users] Adding Hydrogens by pdb2gmx
jmsstarlight at gmail.com
Wed Nov 2 12:41:43 CET 2011
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
e.g ACE is below instead of simple CH3 group
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 ?
3) What another CAP groups in amber tools should I use for capping of termi
wich would be compatible with gromacs ff?
2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>
> James Starlight wrote:
>> all hydrogens were represented as a part of the groupd in wich they were.
>> So is there possible way to explicit it?
> I'm not quite sure I follow. A united atom force field, by definition,
> does not have aliphatic hydrogens. I suggest you consult the literature
> and understand the intrinsics of the chosen force field before you attempt
> to use it.
> Another question about pdb2gmx. about -term
>> as I understood this must be used only if atoms for CAP groups are
>> presented in the PDB file mustnt it?
> The -ter option can be useful in changing the protonation state of the
> termini or in adding caps.
> So what term exactly do? Doest it make a connection beetween CAP and C
>> and N termi or anothing else?
> By default, pdb2gmx builds charged termini (NH3+ and COO-), per the
> typical protonation states of these groups in aqueous solution. If a cap
> is present, then you don't want pdb2gmx doing that, so by choosing "None"
> for the termini in conjunction with the caps, only one proton is added to
> the N-terminus (as in an amide), and only one carbonyl oxygen remains on
> the C-terminus, such that the caps can be added in a sensible way.
> 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
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