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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 !

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