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From: Frank Yan <siebenamber_at_hotmail.com>

Date: Thu 16 Mar 2000 10:43:50 EST

hi... we're using nmode to estimate the entropy of a dna sequence with a

carcinogen binded. we took out the structure from dynamics trajectory, then

do minimization exclude water and ions but using a 4r dd to mimic solvent.

we found that after minimization using a drms of 0.0001 the structure is

extremely distorted to a kind of denatured state, especially at the end the

dna (the base paring are distorted...). it has a rms of 2.7 comparing to the

original structure from dynamics. we think this is an unrealistic state. we

tried to use a less rigorous way to do minimization using drms of 0.01 and

0.1, it turns out that the structure is perfectly well with a rms of 0.7 and

0.4 comparing to the original dynamics structure. but the entropy is kind of

sensitive to this. we want to find minimized structure which is similar to

the dynamics structure, so that we can estimate the entropic term of free

energy of the molecule. i would like to know what the mathematical error

will be if we use a drms of 0.1 or 0.01 in the minimization, then do normal

mode analysis. or is it reasonable to use a less rigorous criteria in

minimization, but to get a much more reasonable or similar structure

comparing to the dynamics structure to get better estimation of entropy.

thanks very much for any help... frank

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Received on Thu Mar 16 2000 - 07:43:50 PST

Date: Thu 16 Mar 2000 10:43:50 EST

hi... we're using nmode to estimate the entropy of a dna sequence with a

carcinogen binded. we took out the structure from dynamics trajectory, then

do minimization exclude water and ions but using a 4r dd to mimic solvent.

we found that after minimization using a drms of 0.0001 the structure is

extremely distorted to a kind of denatured state, especially at the end the

dna (the base paring are distorted...). it has a rms of 2.7 comparing to the

original structure from dynamics. we think this is an unrealistic state. we

tried to use a less rigorous way to do minimization using drms of 0.01 and

0.1, it turns out that the structure is perfectly well with a rms of 0.7 and

0.4 comparing to the original dynamics structure. but the entropy is kind of

sensitive to this. we want to find minimized structure which is similar to

the dynamics structure, so that we can estimate the entropic term of free

energy of the molecule. i would like to know what the mathematical error

will be if we use a drms of 0.1 or 0.01 in the minimization, then do normal

mode analysis. or is it reasonable to use a less rigorous criteria in

minimization, but to get a much more reasonable or similar structure

comparing to the dynamics structure to get better estimation of entropy.

thanks very much for any help... frank

______________________________________________________

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Received on Thu Mar 16 2000 - 07:43:50 PST

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