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Which small molecule to use to model charge distr. in neutral ARG?
#4650 12/16/04 08:17 AM
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??


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Re: Which small molecule to use to model charge distr. in neutral ARG?
chuan #4651 12/20/04 01:46 PM
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RESI MGUA 1.00 ! methyl-guanidinium

as listed in the protein model compound topology file. please make an effort to investigate possible solutions prior to coming to the forum.

alex


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Re: Which small molecule to use to model charge distr. in neutral ARG?
alex #4652 12/21/04 01:19 AM
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What is being looked for is a molecule to convert positive ARG to neutral ARG?

RESI MGUA 1.00 ! methyl-guanidinium is positively charged. I came across that. Thanks anyway.


CHARMM 30b1 driven by 1/ Xeon (32 bits) 2/ Redhat 7.3 (32 bits) with a Quadrics-modified 2.4-18-5 kernel 3/ Chuan, with 95% of the mentorship coming from great scientists frequenting this forum. 4/ Gracious support from the forum.
Re: Which small molecule to use to model charge distr. in neutral ARG?
chuan #4653 12/21/04 01:33 AM
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Quote:

Ed,

The model compound topology file associated with the protein force field
(top_all22_model.inp) contains charges etc. for methylamine (neutral lys)
and phenoxide (ionized tyr) and methylthiolate (ionized cys). Thus, you
are set for those cases. For Arg, the neutral ionization state is not
available; the problem is what proton do you remove????

alex





I quote the above from one old posting. By default, i choose to remove HH22 on ARG. I'll really appreciate help.


CHARMM 30b1 driven by 1/ Xeon (32 bits) 2/ Redhat 7.3 (32 bits) with a Quadrics-modified 2.4-18-5 kernel 3/ Chuan, with 95% of the mentorship coming from great scientists frequenting this forum. 4/ Gracious support from the forum.
Re: Which small molecule to use to model charge distr. in neutral ARG?
chuan #4654 12/21/04 01:17 PM
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the question is, what is the pKa of the sidechain of arginine? which is about 12.5. Thus, it is very rarely deprotonated. In fact I'm not aware of a protein in which a neutral arg has been observed (though I could be wrong). Thus, we have not felt the need to develop a neutral version of the residue. Now, if you still find it necessary to model a neutral arg, then you will have to try modeling it with each of the protons removed. this is due to the four protons being equivalent, such that the proton that would be lost is dependent on the microenvironment around the residue in the protein. not an easy task. good luck.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: Which small molecule to use to model charge distr. in neutral ARG?
alex #4655 12/22/04 02:40 AM
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Hmm... this residue is indeed more trickier than the rest from what i see.


CHARMM 30b1 driven by 1/ Xeon (32 bits) 2/ Redhat 7.3 (32 bits) with a Quadrics-modified 2.4-18-5 kernel 3/ Chuan, with 95% of the mentorship coming from great scientists frequenting this forum. 4/ Gracious support from the forum.
Re: Which small molecule to use to model charge distr. in neutral ARG?
chuan #4656 12/22/04 04:20 PM
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Why do you want to model a neutral arginine?

Re: Which small molecule to use to model charge distr. in neutral ARG?
jb007 #4657 12/24/04 12:59 AM
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There is no specific reason at the moment. The mentality is more like " why isnt neutral ARG easily available??"


CHARMM 30b1 driven by 1/ Xeon (32 bits) 2/ Redhat 7.3 (32 bits) with a Quadrics-modified 2.4-18-5 kernel 3/ Chuan, with 95% of the mentorship coming from great scientists frequenting this forum. 4/ Gracious support from the forum.

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