On 08/30/2011 03:21 PM, David A Case wrote:
> On Tue, Aug 30, 2011, Indrajit Deb wrote:
>
>> I want to prepare single nucleotide. I mean phosphate at the C5'-end and
>> base at C1'. In the all_nuc94.in file RU5, RU3 etc are given, but the
>> problem is that in case of RU3 how to add OH group with the PO2 group at the
>> 5'-end to close the chain and make it a nucleotide. In case of RU5 how to
>> add H at the C3'-end to close the chain and make it nucleoside.
>>
>> I am waiting for helpful suggestions.
> First, I suggest you move to ff10.
>
> If you want a nucleoside, use "UN" ("RUN" in the old nomenclature scheme.)
> If you want a nucleotide, do the following:
>
> loadAmberPrep nucleic10.in (needed since OHE is here, but not in
> nucleic10.lib...needs fixing)
> x = sequence { OHE U3 }
>
> The "x" should be the nucleotide you want.
> (Also to fix: the above should be in the Users' Manual...}
>
> ...hope this helps....dac
>
>
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Hello Dr. Case and AMBER list,
This discussion is relevant to my current work, so I wanted to follow up
with 2 questions:
1. How were the charges for the OHE residue derived?
I don't recall seeing anything about individual nucleotide parameters in
any of the AMBER literature when I first looked (but maybe I missed
something?). Since I didn't find anything at the time I derived my own
charges (using lots of RESP restraints) and got a somewhat less polar OH
group.
2. Will a simulation of a single nucleotide using the parm10 parameters
be stable?
I note that in parm10.dat the HO-OH-P angle parameter has a spring
constant of 45.0, with angle 108.50. My experience with simulations of
single nucleotides using this parameter is that the H on the OH group
makes a beeline for the other phosphate oxygens and bad contacts and
blowups ensue. Others have noted this problem on the listserv in the
past, e.g.:
http://structbio.vanderbilt.edu/archives/amber-archive/2008/2560.php
I did find one ad hoc solution (in addition to Dr. Cheatham's suggestion
on that listserv post) in the literature: The authors of J Mol Model
(2006) 12:281-289 reused the (much stronger spring constant) angle
parameter for the O2-P-O2 angle for the HO-OH-P angle in phosphorylated
amino acids.
Thanks!
Hugh Heldenbrand
Grad Student
University of Minnesota
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Received on Tue Aug 30 2011 - 16:30:04 PDT
