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AMBER Archive (2009)
Subject: [AMBER] inhibitor prepin not recognized in xleap
From: Jayalakshmi Sridhar (jsridhar_at_xula.edu)
Date: Fri Oct 23 2009 - 10:56:40 CDT
- Previous message: Robert Duke: "Re: [AMBER] pmemd ifort problem"
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<div style="font-family: 'Times New Roman'; font-size: 1 6px;">Dear Amber Users,<br _moz_dirty="" />I have = a
protein with a small molecule docked in it. I need to minimize the c omplex. I ran the inhibitor through antechamber to generate prepin and frcmod files. I then loaded the prepin file in xleap and then the com plex pdb file. All help is greatly appreciated. Thanks.<br _ moz_dirty="" /><br _moz_dirty="" />This is the o utput I am getting in xleap:<br _moz_dirty="" /><br _ moz_dirty="" /> 1z10nic = loadpdb 1z10nic_mod5.pdb<br
_moz_dirty="" />= Loading PDB file:
./1z10nic_mod5.pdb<br _moz_dirty=""= /> -- residue
495: duplicate [ C] atoms (total 10)<br _moz_dirt= y=""
/> -- residue 495: duplicate [ H] atoms (total 14)<br
_moz_dirt= y="" /> -- residue 495: duplicate [ N] atoms
(total 2)<br _moz_dirty= ="" /> <br _moz_dirty=""
/> Warning: Atom names in each residue should be unique.<br
_= moz_dirty="" /> (Same-name atoms are handled by
using the first<br _moz= _dirty="" />
occurrence and by ignoring the rest.<br _moz_dir= ty="" />
Frequently duplicate atom names stem from alternate<br _moz_dirty="" /> conformations in the PDB
file.)<br _moz_dirty== "" /> <br _moz_dirty=""
/> One sided connection. Residue: missing connect0 atom.<br
_m= oz_dirty="" /> One sided connection. Residue: missing
connect1 atom.<br _m= oz_dirty="" /> Added missing heavy
atom: .R<CARG 494>.A<= OXT 25><br
_moz_dirty="" /> Added missing heavy atom: .R<NIC
495>.A<C= 1 4><br _moz_dirty="" />
Added missing heavy atom: .R<NIC 495>.A<C= 4
8><br _moz_dirty="" /> Added missing heavy atom:
.R<NIC 495>.A<C= 3 10><br
_moz_dirty="" /> Added missing heavy atom: .R<NIC
495>.A<C= 5 11><br _moz_dirty="" />
Added missing heavy atom: .R<NIC 495>.A<C= 2
1><br _moz_dirty="" /> Added missing heavy atom:
.R<NIC 495>.A<C= 6 13><br
_moz_dirty="" /> Added missing heavy atom: .R<NIC
495>.A<N= 1 22><br _moz_dirty="" />
Added missing heavy atom: .R<NIC 495>.A<C= 7
16><br _moz_dirty="" /> Added missing heavy atom:
.R<NIC 495>.A<C= 8 19><br
_moz_dirty="" /> Added missing heavy atom: .R<NIC
495>.A<C= 9 23><br _moz_dirty=""
/><br _moz_dirty="= " />This is my .prepin file:<br
_moz_dirty="" /> = 0 0 2<br
_moz_dirty="" /><br _= moz_dirty="" />This is a
remark line<br _moz_dirty="= " />molecule.res<br
_moz_dirty="" />NIC INT = 0<br _moz_dirty=""
/>CORRECT OMIT DU BE= G<br _moz_dirty=""
/> 0.0000<br _moz_dirty="= " /> 1 DUMM
DU M 0 -1 -2 = 0.000
.0 .0 = .00000<br
_moz_dirty="" /> 2 DUMM DU = M
1 0 -1 1.449 .0 .0 .00000<br _moz_dirty="" /> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00 000<br _moz_dirty="" /> 4 C2 ca M 3 2 1 1.540 111.208 180.000 0.398300<br _moz_dirty="" /> 5 H2 h4 E 4 3 2 1.082 110.285 152.021 0.023500<br _moz_dirty="" /> 6 N nb M 4 3 2 1.338 132.082 -5.372 -0.667400<br _moz _dirty="" /> 7 C1 ca M 6 4 3 1.334 114.508 -15.311 0. 393700<br _moz_dirty="" /> 8 H1 h4 E 7 6 4 1.081 115.704 171.419 0.022000<br _moz_dirty="" /> 9 C ca M 7 6 4 1.378 122.650 -9.218 -0.249500<br _moz_dirty="" /> 10 H ha E 9 7 6 1.057 124.491 -179.429 0.143600<br _mo z_dirty="" /> 11 C4 ca M 9 7 6 1.358 121.446 3.759 -0 .084900<br _moz_dirty="" /> 12 H3 ha E 11 9 7 1.086 120.269 177.462 0.150100<br _moz_dirty="" /> 13 C3 ca M 11 9 7 1.362 116.419 8.515 -0.193500<br _moz_dirty="" / > 14 C5 c3 M 13 11 9 1.475 118.393 156.894 0.210100<br _moz_dir ty="" /> 15 H4 h1 E 14 13 11 1.089 110.042 90.624 0.068300<b= r
_moz_dirty="" /> 16 C6 c3 M 14 13 11 1.506 110.030 -150.548 -0.10 1800<br _moz_dirty="" /> 17 H5 hc E 16 14 13 1.094 112.449 -93.5 17 0.055800<br _moz_dirty="" /> 18 H6 hc E 16 14 13 1.089 112.965 29.014 0.047000<br _moz_dirty="" /> 19 C7 c3 M 16 14 13 1.480 102.822 145.879 -0.102500<br _moz_dirty="" />=
20 H7 hc E 19 16 14 1. 092 111.815 -110.001 0.047800<br _moz_dirty=" " /> 21 H8 hc E 19 16 14 1.074 105.271 133.653 0.049600<br _moz_ dirty="" /> 22 C8 c3 M 19 16 14 1.519 106.734 9.135 0.14740 0<br _moz_dirty="" /> 23 H9 h1 E 22 19 16 1.093 111.474 80.768 0.055700<br _moz_dirty="" /> 24 H10 h1 E 22 19 16 1.095 114.538 -15 7.270 0.044700<br _moz_dirty="" /> 25 N1 n3 M 22 19 16 1.455 101.4 42 -35.278 -0.704200<br _moz_dirty="" /> 26 C9 c3 M 25 22 19 1.475 109.554 -77.222 0.141400<br _moz_dirty="" /> 27 H11 h1 E 26 25 22 1.0 92 111.860 -163.695 0.049300<br _moz_dirty=" " /> 28 H12 h1 E 26 25 22 1.096 114.117 73.566 0.011700<br _moz_d irty="" /> 29 H13 h1 E 26 25 22 1.097 110.378 -47.999 0.043800<br _moz_dirty="" /><br _moz_dirty="" /><br _m oz_dirty="" />LOOP<br _moz_dirty="" /> C3 C2<br _moz_dirty="" /> N1 C5<br _moz_ dirty="" /><br _moz_dirty="" />IMPROPER<br _mo z_dirty="" /> C3 H2 C2 N<br _mo z_dirty="" /> C H1 C1 N<br _ moz_dirty="" /> C4 C1 C H<br _ moz_dirty="" /> C3 C C4 H3<br _ moz_dirty="" /> C4 C1 C H<br _ moz_dirty="" /> C3 C C4 H3<br _ moz_dirty="" /> C5 C4 C3 C2<br _mo z_dirty="" /><br _moz_dirty="" />DONE<br _mo z_dirty="" />STOP<br _moz_dirty="" /><br _mo z_dirty="" />This is the HETATM in pdb file:<br _moz_d irty="" />HETATM 7585 C NIC 1 57.090 76.668 61.797 1.00 0.00 C<br _moz_dirty="" />HETATM 7586 C NIC 1 58.370 76.789 61.300 1.00 0.00 C<br _moz_dirty="" /> HETATM 7587 N NIC 1 58.868 77. 949 60.869 1.00 0.00 N<br _moz_dirty="" />HETATM 7588 C NIC 1 57.971 78.938 60.776 1.00 0.00 C<br _moz_dirty="" />HETATM 7589 C NIC 1 56.635 78.838 61.14 1 1.00 0.00 C<br _moz_dirt y="" />HETATM 7590 C NIC 1 5 6.231 77.720 61.806 1.00 0.00 C<br _moz_dirty="" />HETATM 7591 C NIC 1 55.606 79.785 60.671 1.00 0.00 C<br _moz_dirty="" /> HETATM 7592 C NIC 1 56.085 80. 494 59.432 1.00 0.00 C<br _moz_dirty="" />HETATM 7593 C NIC 1 54.838 80.678 58.656 1.00 0.00 C<br _moz_dirty="" />HETATM 7594 C NIC 1 53.691 80.283 59.57 1 1.00 0.00 C<br _moz_dirt y="" />HETATM 7595 N NIC 1 5 4.286 79.189 60.324 1.00 0.00 N<br _moz_dirty="" />HETATM 7596 C NIC 1 54.310 77.972 59.491 1.00 0.00 C<br _moz_dirty="" /> HETATM 7597 H NIC 1 56.669 75. 766 62.154 1.00 0.00 H<br _moz_dirty="" />HETATM 7598 H NIC 1 59.040 75.942 61.246 1.00 0.00 H<br _moz_dirty="" />HETATM 7599 H NIC 1 58.346 79.834 60.30 0 1.00 0.00 H<br _moz_dirt y="" />HETATM 7600 H NIC 1 5 5.214 77.593 62.164 1.00 0.00 H<br _moz_dirty="" />HETATM 7601 H NIC 1 55.414 80.537 61.435 1.00 0.00 H<br _moz_dirty="" /> HETATM 7602 H NIC 1 56.571 81. 448 59.658 1.00 0.00 H<br _moz_dirty="" />HETATM 7603 H NIC 1 56.777 79.896 58.841 1.00 0.00 H<br _moz_dirty="" />HETATM 7604 H NIC 1 54.817 80.046 57.76 6 1.00 0.00 H<br _moz_dirt y="" />HETATM 7605 H NIC 1 5 4.859 81.699 58.325 1.00 0.00 H<br _moz_dirty="" />HETATM 7606 H NIC 1 53.431 81.092 60.259 1.00 0.00 H<br _moz_dirty="" /> HETATM 7607 H NIC 1 52.773 79. 993 59.050 1.00 0.00 H<br _moz_dirty="" />HETATM 7608 H NIC 1 54.476 77.073 60.089 1.00 0.00 H<br _moz_dirty="" />HETATM 7609 H NIC 1 55.063 77.989 58.69 5 1.00 0.00 H<br _moz_dirt y="" />HETATM 7610 H NIC 1 5 3.331 77.810 59.023 1.00 0.00 H<br _moz_dirty="" /><br _moz_dirty="" />Jaya.<br /></div>
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