Hi all,
I am a little nervous about the dihedral terms I just found in one of my
prmtop files for a system with DNA (built with the amberff99SB-ILDN force
field). Below I show all the dihedrals for a CYT residue (I haven't
checked if this problem is occurring in other residues or in other force
fields). Note the entries that I have marked '#' or '##' or '###', these
are the terms I am questioning. From what I understand, any term that
begins with 'E' extends the definition of the dihedral term preceding it.
Is that correct? If that's the case, then it would only make sense that
the atoms which define the term would have to be exactly the same in each
row. Is that correct?
If both of my assertions above are correct, then there is a big problem
because the dihedrals I have marked '#' or '##' or '###' do not follow
those rules. Is this a bug in tleap?
If on the other hand, these entries below are allowed, could someone please
explain to me what they mean, because I am confused if this is designed
this way. Thank you for your help.
Sid
PS. The majority of the terms marked with '#'s below include the C4 atom
or C3' atom.
RDPARM MENU: dihedrals :90
Mask [:90] represents 30 atoms
Dihedral pk phase pn atoms
3335: 0.383 0.00 3.0 :89.H3' :89.C3' :89.O3' :90.P
(1713,1712,1717,1718)
3380: 0.250 0.00 1.0 :90.H2'2 :90.C2' :90.C3' :90.O3'
(1746,1744,1742,1747)
E 3381: 0.000 0.00 3.0 :90.H2'2 :90.C2' :90.C3' :90.O3'
(1746,1744,1742,1747)
3382: 0.250 0.00 1.0 :90.H2'1 :90.C2' :90.C3' :90.O3'
(1745,1744,1742,1747)
E 3383: 0.000 0.00 3.0 :90.H2'1 :90.C2' :90.C3' :90.O3'
(1745,1744,1742,1747)
3384: 0.156 0.00 3.0 :90.H3' :90.C3' :90.C2' :90.H2'1
(1743,1742,1744,1745)
3385: 0.156 0.00 3.0 :90.H3' :90.C3' :90.C2' :90.H2'2
(1743,1742,1744,1746)
3386: 0.383 0.00 3.0 :90.H3' :90.C3' :90.O3' :91.P
(1743,1742,1747,1748)
3387: 2.400 3.14 2.0 :90.H42 :90.N4 :90.C4 :90.N3
(1738,1736,1735,1739)
3388: 2.400 3.14 2.0 :90.H41 :90.N4 :90.C4 :90.N3
(1737,1736,1735,1739)
3389: 2.550 3.14 2.0 :90.H5 :90.C5 :90.C4 :90.N4
(1734,1733,1735,1736)
3390: 2.550 3.14 2.0 :90.H5 :90.C5 :90.C4 :90.N3
(1734,1733,1735,1739)
3391: 2.400 3.14 2.0 :90.C5 :90.C4 :90.N4 :90.H41
(1733,1735,1736,1737)
3392: 2.400 3.14 2.0 :90.C5 :90.C4 :90.N4 :90.H42
(1733,1735,1736,1738)
3393: 1.850 3.14 2.0 :90.H6 :90.C6 :90.N1 :90.C2
(1732,1731,1730,1740)
3394: 6.650 3.14 2.0 :90.H6 :90.C6 :90.C5 :90.H5
(1732,1731,1733,1734)
3395: 6.650 3.14 2.0 :90.H6 :90.C6 :90.C5 :90.C4
(1732,1731,1733,1735)
3396: 0.156 0.00 3.0 :90.N1 :90.C1' :90.C2' :90.H2'1
(1730,1728,1744,1745)
3397: 0.156 0.00 3.0 :90.N1 :90.C1' :90.C2' :90.H2'2
(1730,1728,1744,1746)
3398: 6.650 3.14 2.0 :90.N1 :90.C6 :90.C5 :90.H5
(1730,1731,1733,1734)
3399: 0.000 0.00 2.0 :90.H1' :90.C1' :90.N1 :90.C6
(1729,1728,1730,1731)
3400: 0.000 0.00 2.0 :90.H1' :90.C1' :90.N1 :90.C2
(1729,1728,1730,1740)
3401: 0.156 0.00 3.0 :90.H1' :90.C1' :90.C2' :90.C3'
(1729,1728,1744,1742)
3402: 0.156 0.00 3.0 :90.H1' :90.C1' :90.C2' :90.H2'1
(1729,1728,1744,1745)
3403: 0.156 0.00 3.0 :90.H1' :90.C1' :90.C2' :90.H2'2
(1729,1728,1744,1746)
3404: 1.850 3.14 2.0 :90.C1' :90.N1 :90.C6 :90.H6
(1728,1730,1731,1732)
3405: 0.156 0.00 3.0 :90.C1' :90.C2' :90.C3' :90.H3'
(1728,1744,1742,1743)
3406: 0.250 0.00 1.0 :90.O4' :90.C4' :90.C3' :90.H3'
(1727,1725,1742,1743)
E 3407: 0.000 0.00 3.0 :90.O4' :90.C4' :90.C3' :90.H3'
(1727,1725,1742,1743)
3408: 0.250 0.00 1.0 :90.O4' :90.C1' :90.C2' :90.H2'1
(1727,1728,1744,1745)
E 3409: 0.000 0.00 3.0 :90.O4' :90.C1' :90.C2' :90.H2'1
(1727,1728,1744,1745)
3410: 0.250 0.00 1.0 :90.O4' :90.C1' :90.C2' :90.H2'2
(1727,1728,1744,1746)
E 3411: 0.000 0.00 3.0 :90.O4' :90.C1' :90.C2' :90.H2'2
(1727,1728,1744,1746)
3412: 0.383 0.00 3.0 :90.H4' :90.C4' :90.O4' :90.C1'
(1726,1725,1727,1728)
3413: 0.156 0.00 3.0 :90.H4' :90.C4' :90.C3' :90.H3'
(1726,1725,1742,1743)
3414: 0.156 0.00 3.0 :90.H4' :90.C4' :90.C3' :90.C2'
(1726,1725,1742,1744)
3415: 0.250 0.00 1.0 :90.H4' :90.C4' :90.C3' :90.O3'
(1726,1725,1742,1747)
E 3416: 0.000 0.00 3.0 :90.H4' :90.C4' :90.C3' :90.O3'
(1726,1725,1742,1747)
3417: 0.383 0.00 3.0 :90.C4' :90.O4' :90.C1' :90.H1'
(1725,1727,1728,1729)
3418: 0.160 0.00 3.0 :90.C4' :90.C3' :90.C2' :90.H2'1
(1725,1742,1744,1745)
3419: 0.160 0.00 3.0 :90.C4' :90.C3' :90.C2' :90.H2'2
(1725,1742,1744,1746)
3420: 0.156 0.00 3.0 :90.H5'2 :90.C5' :90.C4' :90.H4'
(1724,1722,1725,1726)
3421: 0.250 0.00 1.0 :90.H5'2 :90.C5' :90.C4' :90.O4'
(1724,1722,1725,1727)
E 3422: 0.000 0.00 3.0 :90.H5'2 :90.C5' :90.C4' :90.O4'
(1724,1722,1725,1727)
3423: 0.156 0.00 3.0 :90.H5'2 :90.C5' :90.C4' :90.C3'
(1724,1722,1725,1742)
3424: 0.156 0.00 3.0 :90.H5'1 :90.C5' :90.C4' :90.H4'
(1723,1722,1725,1726)
3425: 0.250 0.00 1.0 :90.H5'1 :90.C5' :90.C4' :90.O4'
(1723,1722,1725,1727)
E 3426: 0.000 0.00 3.0 :90.H5'1 :90.C5' :90.C4' :90.O4'
(1723,1722,1725,1727)
3427: 0.156 0.00 3.0 :90.H5'1 :90.C5' :90.C4' :90.C3'
(1723,1722,1725,1742)
3428: 0.156 0.00 3.0 :90.C5' :90.C4' :90.C3' :90.H3'
(1722,1725,1742,1743)
3429: 0.250 0.00 1.0 :90.O5' :90.C5' :90.C4' :90.H4'
(1721,1722,1725,1726)
E 3430: 0.000 0.00 3.0 :90.O5' :90.C5' :90.C4' :90.H4'
(1721,1722,1725,1726)
3431: 0.383 0.00 3.0 :90.P :90.O5' :90.C5' :90.H5'1
(1718,1721,1722,1723)
3432: 0.383 0.00 3.0 :90.P :90.O5' :90.C5' :90.H5'2
(1718,1721,1722,1724)
B 3715: 1.000 3.14 2.0 :90.C4 :90.H41 :90.N4 :90.H42
(1735,1737,1736,1738)
B 3716: 1.100 3.14 2.0 :90.C6 :90.C4 :90.C5 :90.H5
(1731,1735,1733,1734)
B 3717: 1.100 3.14 2.0 :90.N1 :90.C5 :90.C6 :90.H6
(1730,1733,1731,1732)
6619: 1.200 0.00 2.0 :89.O3' :90.P :90.O5' :90.C5'
(1717,1718,1721,1722)
E 6620: 0.250 0.00 3.0 :89.O3' :90.P :90.O5' :90.C5'
(1717,1718,1721,1722)
6621: 0.383 0.00 3.0 :89.C2' :89.C3' :89.O3' :90.P
(1714,1712,1717,1718)
6622: 0.250 0.00 3.0 :89.C3' :89.O3' :90.P :90.O1P
(1712,1717,1718,1719)
6623: 0.250 0.00 3.0 :89.C3' :89.O3' :90.P :90.O2P
(1712,1717,1718,1720)
6624: 1.200 0.00 2.0 :89.C3' :89.O3' :90.P :90.O5'
(1712,1717,1718,1721)
E 6625: 0.250 0.00 3.0 :89.C3' :89.O3' :90.P :90.O5'
(1712,1717,1718,1721)
6669: 0.383 0.00 3.0 :89.C4' :89.C3' :89.O3' :90.P
(1693,1712,1717,1718)
6682: 1.200 0.00 2.0 :90.O3' :91.P :91.O5' :91.C5'
(1747,1748,1751,1752)
E 6683: 0.250 0.00 3.0 :90.O3' :91.P :91.O5' :91.C5'
(1747,1748,1751,1752)
6684: 0.383 0.00 3.0 :90.C2' :90.C3' :90.O3' :91.P
(1744,1742,1747,1748)
6685: 0.250 0.00 3.0 :90.C3' :90.O3' :91.P :91.O1P
(1742,1747,1748,1749)
6686: 0.250 0.00 3.0 :90.C3' :90.O3' :91.P :91.O2P
(1742,1747,1748,1750)
6687: 1.200 0.00 2.0 :90.C3' :90.O3' :91.P :91.O5'
(1742,1747,1748,1751)
E 6688: 0.250 0.00 3.0 :90.C3' :90.O3' :91.P :91.O5'
(1742,1747,1748,1751)
6689: 0.000 0.00 2.0 :90.C2 :90.N1 :90.C1' :90.C2'
(1740,1730,1728,1744)
6690: 4.800 3.14 2.0 :90.N4 :90.C4 :90.N3 :90.C2
(1736,1735,1739,1740)
6691: 4.000 3.14 2.0 :90.C4 :90.N3 :90.C2 :90.O2
(1735,1739,1740,1741)
6692: 1.850 3.14 2.0 :90.C5 :90.C6 :90.N1 :90.C2
(1733,1731,1730,1740) #
E 6693: 4.800 3.14 2.0 :90.C5 :90.C4 :90.N3 :90.C2
(1733,1735,1739,1740) #
6694: 0.000 0.00 2.0 :90.C6 :90.N1 :90.C1' :90.C2'
(1731,1730,1728,1744)
6695: 1.450 3.14 2.0 :90.C6 :90.N1 :90.C2 :90.N3
(1731,1730,1740,1739)
6696: 1.450 3.14 2.0 :90.C6 :90.N1 :90.C2 :90.O2
(1731,1730,1740,1741)
6697: 2.550 3.14 2.0 :90.C6 :90.C5 :90.C4 :90.N4
(1731,1733,1735,1736) #
E 6698: 2.550 3.14 2.0 :90.C6 :90.C5 :90.C4 :90.N3
(1731,1733,1735,1739) #
6699: 0.156 0.00 3.0 :90.N1 :90.C1' :90.C2' :90.C3'
(1730,1728,1744,1742)
6700: 6.650 3.14 2.0 :90.N1 :90.C6 :90.C5 :90.C4
(1730,1731,1733,1735) #
E 6701: 4.000 3.14 2.0 :90.N1 :90.C2 :90.N3 :90.C4
(1730,1740,1739,1735) #
E 6702: 0.100 3.14 2.0 :90.C1' :90.O4' :90.C4' :90.C3'
(1728,1727,1725,1742) ##
E 6703: 0.383 0.00 3.0 :90.C1' :90.O4' :90.C4' :90.C3'
(1728,1727,1725,1742) ##
6704: 1.850 3.14 2.0 :90.C1' :90.N1 :90.C6 :90.C5
(1728,1730,1731,1733)
6705: 1.450 3.14 2.0 :90.C1' :90.N1 :90.C2 :90.N3
(1728,1730,1740,1739)
6706: 1.450 3.14 2.0 :90.C1' :90.N1 :90.C2 :90.O2
(1728,1730,1740,1741)
6707: 0.156 0.00 3.0 :90.C1' :90.C2' :90.C3' :90.O3'
(1728,1744,1742,1747) #
E 6708: 0.156 0.00 3.0 :90.O4' :90.C4' :90.C3' :90.C2'
(1727,1725,1742,1744) #
6709: 1.175 0.00 2.0 :90.O4' :90.C4' :90.C3' :90.O3'
(1727,1725,1742,1747)
E 6710: 0.144 0.00 3.0 :90.O4' :90.C4' :90.C3' :90.O3'
(1727,1725,1742,1747)
6711: 2.500 0.00 1.0 :90.O4' :90.C1' :90.N1 :90.C6
(1727,1728,1730,1731)
E 6712: 0.000 0.00 2.0 :90.O4' :90.C1' :90.N1 :90.C6
(1727,1728,1730,1731)
6713: 0.000 0.00 2.0 :90.O4' :90.C1' :90.N1 :90.C2
(1727,1728,1730,1740) #
E 6714: 0.156 0.00 3.0 :90.O4' :90.C1' :90.C2' :90.C3'
(1727,1728,1744,1742) #
6715: 0.650 0.00 2.0 :90.C4' :90.O4' :90.C1' :90.N1
(1725,1727,1728,1730)
E 6716: 0.383 0.00 3.0 :90.C4' :90.O4' :90.C1' :90.N1
(1725,1727,1728,1730)
E 6717: 0.100 3.14 2.0 :90.C4' :90.O4' :90.C1' :90.C2'
(1725,1727,1728,1744) ###
E 6718: 0.383 0.00 3.0 :90.C4' :90.O4' :90.C1' :90.C2'
(1725,1727,1728,1744) ###
E 6719: 0.200 3.14 1.0 :90.C4' :90.C3' :90.C2' :90.C1'
(1725,1742,1744,1728) ###
E 6720: 0.250 3.14 2.0 :90.C4' :90.C3' :90.C2' :90.C1'
(1725,1742,1744,1728) ###
E 6721: 0.180 0.00 3.0 :90.C4' :90.C3' :90.C2' :90.C1'
(1725,1742,1744,1728) ###
6722: 0.383 0.00 3.0 :90.C4' :90.C3' :90.O3' :91.P
(1725,1742,1747,1748)
6723: 0.100 3.14 2.0 :90.C5' :90.C4' :90.O4' :90.C1'
(1722,1725,1727,1728)
E 6724: 0.383 0.00 3.0 :90.C5' :90.C4' :90.O4' :90.C1'
(1722,1725,1727,1728)
6725: 0.200 3.14 1.0 :90.C5' :90.C4' :90.C3' :90.C2'
(1722,1725,1742,1744)
E 6726: 0.250 3.14 2.0 :90.C5' :90.C4' :90.C3' :90.C2'
(1722,1725,1742,1744)
E 6727: 0.180 0.00 3.0 :90.C5' :90.C4' :90.C3' :90.C2'
(1722,1725,1742,1744)
6728: 0.156 0.00 3.0 :90.C5' :90.C4' :90.C3' :90.O3'
(1722,1725,1742,1747)
6729: 1.175 0.00 2.0 :90.O5' :90.C5' :90.C4' :90.O4'
(1721,1722,1725,1727)
E 6730: 0.144 0.00 3.0 :90.O5' :90.C5' :90.C4' :90.O4'
(1721,1722,1725,1727)
6731: 0.156 0.00 3.0 :90.O5' :90.C5' :90.C4' :90.C3'
(1721,1722,1725,1742)
6732: 0.250 0.00 3.0 :90.O2P :90.P :90.O5' :90.C5'
(1720,1718,1721,1722)
6733: 0.250 0.00 3.0 :90.O1P :90.P :90.O5' :90.C5'
(1719,1718,1721,1722)
6734: 0.383 0.00 3.0 :90.P :90.O5' :90.C5' :90.C4'
(1718,1721,1722,1725)
B 7004: 10.500 3.14 2.0 :90.N1 :90.N3 :90.C2 :90.O2
(1730,1739,1740,1741)
B 7005: 1.100 3.14 2.0 :90.C5 :90.N4 :90.C4 :90.N3
(1733,1736,1735,1739)
B 7006: 1.000 3.14 2.0 :90.C2 :90.C6 :90.N1 :90.C1'
(1740,1731,1730,1728)
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Received on Tue May 06 2014 - 10:30:03 PDT
