Dear Sir/Madam,
I have done a torsion angle restrainst for a DNA base pairs to mimic the twist angle changing process. I define my twist angle as <1234
2-----1
|
3-----4
and set the restrainst as follows:
# angle restraint
&rst iat=1,2,3,4, r1=-180.0, r2=90.0, r3=90.0, r4=180.0, rk2 =70.0, rk3 =70.,
igr1=9742,9743,9744,9745,9746,9747,9748,9749,9750,9751,9752,9753,9754,9755,9756,9757,9758,9759,9760,9761,9762,9763,9764,9765,9766,9767,9768,9769,9770,9771,9772,9773,0,
igr2=10537,10538,10539,10540,10541,10542,10543,10544,10545,10546,10547,10548,10549,10550,10551,10552,10553,10554,10555,10556,10557,10558,10559,10560,10561,10562,10563,10564,10565,10566,10567,10568,0,
igr3=10507,10508,10509,10510,10511,10512,10513,10514,10515,10516,10517,10518,10519,10520,10521,10522,10523,10524,10525,10526,10527,10528,10529,10530,10531,10532,10533,10534,10535,10536,0,
igr4=9774,9775,9776,9777,9778,9779,9780,9781,9782,9783,9784,9785,9786,9787,9788,9789,9790,9791,9792,9793,9794,9795,9796,9797,9798,9799,9800,9801,9802,9803,9804,0/
where igr1, igr2, igr3, igr4 is all the atoms (both heavy and hydrogen atoms) in base 1, 2, 3, 4, respectively.
I change the twist angle from -180 to 180.
As I am doing PMF, the twist angle changes during the tracjectory was dumped to the results files. When I open the result files, I found the angles has been changed accordingly, i.e. the when restrainst of 180 was used, the result file see ~180, when restrainst of -180 was used, the result file was around -180. Accordingly, expected results were obtained for others windows.
However, when I open the structures of the vmd, I found the base pairs did not flip around at all.
When I use ptraj to generate the average structures for 180 and -180 restrainst. They are almost the same. I used the accelyr to define the cetnroid atoms for igr1, igr2, igr3 and igr4, and monitor the torison angle of these centroid atoms. I found the torison angle are remain the same too.
Did I used the wrong way to define the twist angle based on DOC? Pls kindly comments.
Best regards,
Catherine.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 18 2010 - 21:30:03 PDT
