Justin,<br><br>Could you tell me more about adding caps by amber tools?<br><br>1) I've found in that software ACE as well as other groups but they are not standart<br><br>e.g ACE is below instead of simple CH3 group<br>
949 HH31 ACE 29 2.000 1.000 -0.000 1.00 0.00<br>ATOM 950 CH3 ACE 29 2.000 2.090 0.000 1.00 0.00<br>ATOM 951 HH32 ACE 29 1.486 2.454 0.890 1.00 0.00<br>ATOM 952 HH33 ACE 29 1.486 2.454 -0.890 1.00 0.00<br>
ATOM 953 C ACE 29 3.427 2.641 -0.000 1.00 0.00<br>ATOM 954 O ACE 29 4.391 1.877 -0.000 1.00 0.00<br>ATOM 955 H7 ACE 29 3.582 3.629 -0.000 1.00 0.00<br><br>have you edited that group to standart form in amber tools or used something else ?<br>
<br>2) How you place CAP groups to desired coordinates?<br>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 ?<br>
<br>3) What another CAP groups in amber tools should I use for capping of termi wich would be compatible with gromacs ff?<br><br>James<br><br><div class="gmail_quote">2011/10/31 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
exactly<br>
<br>
all hydrogens were represented as a part of the groupd in wich they were. So is there possible way to explicit it?<br>
<br>
</blockquote>
<br></div>
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.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Another question about pdb2gmx. about -term<br>
as I understood this must be used only if atoms for CAP groups are presented in the PDB file mustnt it?<br>
</blockquote>
<br></div>
The -ter option can be useful in changing the protonation state of the termini or in adding caps.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
So what term exactly do? Doest it make a connection beetween CAP and C and N termi or anothing else?<br>
<br>
</blockquote>
<br></div>
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.<div>
<div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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