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where can I find the parameters about GC pair
#18529 07/15/08 03:07 AM
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ckc1117 Offline OP
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Dear all:
I read the paper "Performance of Empirical Potentials
(AMBER, CFF95, CVFF, CHARMM,OPLS, POLTEV), Semiempirical
Quantum Chemical Methods (AM1,MNDO/ M, PM3), and Ab Initio
Hartree]Fock Method for Interaction of DNA Bases: Comparison with Nonempirical Beyond Hartree]Fock Results" publish on jcc 1996
I am intested in the H-bonded GC base pairs. and the author mentioned them in the supporting information. but I didn't find the right parameter for it withou the sidechain. if anybody knows, please tell me about it , thank you very much!

Re: where can I find the parameters about GC pair
ckc1117 #18530 07/15/08 05:02 PM
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rmv Online Content
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You may need to be more specific about what you are looking for, and you may also need to look a little more for yourself, perhaps in the toppar/stream subdir ...

Re: where can I find the parameters about GC pair
rmv #18531 07/16/08 01:54 AM
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Dear rmv:
What I want is the H-bonded GC pair without the sidechain.

H6
\
O6
|
C6
// \
N1 C5--N7\\
| || C8-H8
C2 C4--N9/
/ \\ / \
H21-N2 N3 \
| \
H22 H9


and

H41
\
N4
||
C4
/ \
H3-N3 C5-H5
| ||
C2 C6
//\ / \
O2 N1 H6
|
H1


I will look into the toppar/stream subdir and find it .
thank you sir!

the picture is bad , so I put a snapshot of GC pair I want in the attachment:)

Attached Files
18693-snap.jpg (0 Bytes, 311 downloads)
Last edited by ckc1117; 07/16/08 02:00 AM.
Re: where can I find the parameters about GC pair
ckc1117 #18532 07/16/08 02:27 AM
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G and C are the sidechains on the phospho-(deoxy)ribose backbone of nucleic acid polymers; the context of "G w/o sidechain" was vague.

Model compounds, esp. fragments, are usually found in toppar/stream of the CHARMM distribution.

The wise student would have looked there already.

Re: where can I find the parameters about GC pair
rmv #18533 07/29/08 03:30 AM
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Dear sir:
thank you for your reply. what I mean G/C pair is the guanine and the cytosine, and I want to do MD simulation about H-bonded G/C pairs.
Now, I don't find the right topology for these. but there are tautomers in toppar/stream subdir. and they are not the one I need.
is it possible that I just delete the sidechain and add H atom for Guanine and Cytosine ? and is it Ok if I care the H-bond much ?
thank you for your help!

Re: where can I find the parameters about GC pair
ckc1117 #18534 07/29/08 06:36 PM
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Please read the files more carefully; the "all27_na_model" file has patches to remove the sugar and phosphate atoms and provide the individual purine or pyrimidine bases.

I don't understand all your comments about H-bonds; if the molecules are aligned properly, the charge and VDW interactions should facilitate a stable interaction.

Re: where can I find the parameters about GC pair
rmv #18535 07/31/08 01:50 AM
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thank you sir! I will try to do the patch work , thank you

Re: where can I find the parameters about GC pair
rmv #18536 08/01/08 10:13 AM
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Dear sir, the simulation is going well now, thanks very much ! but here comes another problem : the G/C base were initially placed in a plane , but after a serial of minimization in the water box, they become perpendicular. is it normal ? how can this happen ? is it something to do with the vdW parameter or something else ?
thank you very much !

Re: where can I find the parameters about GC pair
ckc1117 #18537 08/01/08 06:04 PM
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Although H-bonds stabilize the double helix, H-bonds alone may not make the G-C and A-T pairs stable individually, w/o the DNA scaffolding. The free bases in solution have too many other degrees of freedom available. Water will also form H-bonds with the polar parts of the bases.

Re: where can I find the parameters about GC pair
rmv #18538 08/02/08 01:49 AM
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roger that, thank you sir
but what do you mean about "w/o the DNA scaffolding" ? is it some way to enforce them on a plane ? maybe I shall go on the equilibrium step, they might be on a plane after a long time and become stable.
thank you very much !

Re: where can I find the parameters about GC pair
ckc1117 #18539 08/02/08 03:28 AM
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I mean that the phosphodeoxyribose backbone and additional base pairs are needed to get stable H-bonds. Experimentally, most biological helices require a couple turns of the helix in order to be stable in aqueous solution.

Re: where can I find the parameters about GC pair
rmv #18540 08/03/08 02:59 AM
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I see others's work (year 1997) using CHARMM23 parameter doing MD of the GC pair are quite stable , after MD simulation, the two bases are in a plane, but in my case, during 1ns equilibrium step, the G-C pair flying apart though they are H-bonded in the first 250ps. is it something to do with the initial sturcture ? and is it any way to make them more stable in a plane ?
thank you very much !

Re: where can I find the parameters about GC pair
ckc1117 #18541 08/03/08 05:34 PM
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Perhaps there are some differences between your setup and what was used in the paper; you'll have to look into that more carefully.

I do not recommend using restraints to impose your expectation of what the results should be; that's known as biasing the results.

Re: where can I find the parameters about GC pair
rmv #18542 08/04/08 12:57 PM
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you are right, I shall take more respect of the results.
in the paper mentioned above, they didn't mention the solvation box, they should just do it only with base pairs.
but what shall I do with my simulation of G-C pair in water box, it seems all right that the bases fly apart or they form stacking but not pair during equilibrium step. but I can't perform vibrational analysis to check the H-bond effect on the sturcture.
but is it still meaningful go on the simulation and check the sturctural fluctuation?
and by the way, is there any already published paper about base pair simulation ? I didn't find about G-C pair yet.
thank you for your time !

Last edited by ckc1117; 08/04/08 12:58 PM.
Re: where can I find the parameters about GC pair
ckc1117 #18543 08/04/08 04:47 PM
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It has been said that six months of effort (lab experiments, or modeling and computer time) can save you a day in the library.

Are there any experimental papers that suggest the isolated G and C free bases form long lasting H-bonded stable complexes in aqueous solution?

I should note perhaps a new post (after some library research on your part) in another forum may be called for; this is no longer about G, C parameters ...

Re: where can I find the parameters about GC pair
rmv #18544 08/05/08 01:24 AM
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I am really rush into these works, and did not take enough time to do the research. it is really not good.
thank you for reminding me sir!

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