I did some more checking and this is happening with all other DNA residues:
DG, DA, DT, DC5, DC3, DG5, and DG3. Also, I am using AmberTools13,
installed with patches as of beginning of March 2014. I also checked a few
protein residues: NGLU, SER, GLY, LYS, and ARG and this doesn't appear to
be happening for proteins (should do a more exhaustive check).
On Tue, May 6, 2014 at 10:04 AM, Sidney Elmer <paulymer.gmail.com> wrote:
> 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 - 11:00:04 PDT
