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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 - 11:05:46 CDT
- Previous message: Jayalakshmi Sridhar: "[AMBER] inhibitor prepin not recognized in xleap"
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<![endif]--> <p class="MsoNormal">Dear Amber
Users,<br /> I am resending my earlier mail as it did not go through
properly. Hope= this does not get scrambled. Sorry about this.<br
_moz_dirty== "" /></p><p _moz_dirty=""
class="MsoNormal">= I have a protein with a small molecule docked in
it. I need to minimiz= e the complex. I ran the inhibitor through
antechamber to generate prepin an= d frcmod files. I then loaded the
prepin file in xleap and then the complex pdb= file. All help is
greatly appreciated. Thanks.<br /> <br /> This is the output I
am getting in xleap:<br /> <br /> 1z10nic = loadpdb
1z10nic_mod5.pdb<br /> Loading PDB file:
./1z10nic_mod5.pdb<br /> -- residue 495: duplicate [ C]
atoms (total 10)<br /> -- residue 495: duplicate [ H] atoms (total
14)<br /> -- residue 495: duplicate [ N] atoms (total 2)<br />
<br /> Warning: Atom names in each residue should be
unique.<br />= (Same-name atoms are handled by using the
first<br /> occurrence and by ignoring the rest.<br
/> Frequently duplicate atom names stem from
alternate<br /> conformations in the PDB file.)<br
/> <br /> One sided connection. Residue: missing connect0
atom.<br />= One sided connection. Residue: missing connect1
atom.<br />= Added missing heavy atom: .R<CARG
494>.A<= OXT 25><br /> Added missing heavy
atom: .R<NIC 495>.A<C= 1 4><br />
Added missing heavy atom: .R<NIC 495>.A<C= 4
8><br /> Added missing heavy atom: .R<NIC
495>.A<C= 3 10><br /> Added missing heavy
atom: .R<NIC 495>.A<C= 5 11><br />
Added missing heavy atom: .R<NIC 495>.A<C= 2
1><br /> Added missing heavy atom: .R<NIC
495>.A<C= 6 13><br /> Added missing heavy
atom: .R<NIC 495>.A<N= 1 22><br />
Added missing heavy atom: .R<NIC 495>.A<C= 7
16><br /> Added missing heavy atom: .R<NIC
495>.A<C= 8 19><br /> Added missing heavy
atom: .R<NIC 495>.A<C= 9 23><br />
<br /> This is my .prepin file:<br /> 0
0 2<br /> <br /> This is a remark line<br />
molecule.res<br /> NIC INT 0<br /> CORRECT
OMIT DU BEG<br /> 0.0000<br /> 1 DUMM
DU M 0 -1 -2 0.000
.0 .0 .00000<br /> 2
DUMM DU M 1 0 -1
1.449 .0 .0
.00000<br /> 3 DUMM DU M 2
1 0 1.522 111.1
.0 .00000<br /> 4 C2 ca
M 3 2 1 1.540 111.208
180.000 0.398300<br /> 5 H2 h4
E 4 3 2 1.082 110.285
152.021 0.023500<br /> 6 N nb
M 4 3 2 1.338 132.082
-5.372 -0.667400<br /> 7 C1 ca
M 6 4 3 1.334 114.508
-15.311 0.393700<br /> 8 H1 h4
E 7 6 4 1.081 115.704
171.419 0.022000<br /> 9 C ca
M 7 6 4 1.378 122.650
-9.218 -0.249500<br /> 10 H ha
E 9 7 6 1.057 124.491
-179.429 0.143600<br /> 11 C4 ca
M 9 7 6 1.358 121.446
3.759 -0.084900<br /> 12 H3 ha E
11 9 7 1.086 120.269 177.462
0.150100<br /> 13 C3 ca M 11
9 7 1.362 116.419 8.515
-0.193500<br /> 14 C5 c3 M 13
11 9 1.475 118.393 156.894
0.210100<br /> 15 H4 h1 E 14 13
11 1.089 110.042 90.624 0.068300<br
/> 16 C6 c3 M 14 13 11
1.506 110.030 -150.548 -0.101800<br /> 17
H5 hc E 16 14 13 1.094
112.449 -93.517 0.055800<br /> 18 H6
hc E 16 14 13 1.089
112.965 29.014 0.047000<br /> 19 C7
c3 M 16 14 13 1.480 102.822
145.879 -0.102500<br /> 20 H7 hc E
19 16 14 1.092 111.815 -110.001
0.047800<br /> 21 H8 hc E 19 16
14 1.074 105.271 133.653 0.049600<br
/> 22 C8 c3 M 19 16 14
1.519 106.734 9.135 0.147400<br />
23 H9 h1 E 22 19 16
1.093 111.474 80.768 0.055700<br /> 24
H10 h1 E 22 19 16 1.095
114.538 -157.270 0.044700<br /> 25 N1
n3 M 22 19 16 1.455 101.442
-35.278 -0.704200<br /> 26 C9 c3 M
25 22 19 1.475 109.554 -77.222
0.141400<br /> 27 H11 h1 E 26 25
22 1.092 111.860 -163.695 0.049300<br />
28 H12 h1 E 26 25 22
1.096 114.117 73.566 0.011700<br /> 29
H13 h1 E 26 25 22 1.097
110.378 -47.999 0.043800<br /> <br /> <br />
LOOP<br /> C3 C2<br /> N1 C5<br />
<br /> IMPROPER<br /> C3 H2 C2 N<br
/> C H1 C1 N<br /> C4
C1 C H<br /> C3 C C4
H3<br /> C4 C1 C H<br />
C3 C C4 H3<br /> C5 C4 C3
C2<br /> <br /> DONE<br /> STOP<br /> <br /> This is the
HETATM in pdb file:<br /> HETATM 7585 C NIC
1 57.090 76.668 61.797 1.00
0.00 C<br /> HETATM 7586 C
NIC 1 58.370 76.789 61.300
1.00 0.00 C<br /> HETATM 7587
N NIC 1 58.868 77.949 60.869
1.00 0.00 N<br /> HETATM 7588
C NIC 1 57.971 78.938 60.776
1.00 0.00 C<br /> HETATM 7589
C NIC 1 56.635 78.838 61.141
1.00 0.00 C<br /> HETATM 7590
C NIC 1 56.231 77.720 61.806
1.00 0.00 C<br /> HETATM 7591
C NIC 1 55.606 79.785 60.671
1.00 0.00 C<br /> HETATM 7592
C NIC 1 56.085 80.494 59.432
1.00 0.00 C<br /> HETATM 7593
C NIC 1 54.838 80.678 58.656
1.00 0.00 C<br /> HETATM 7594
C NIC 1 53.691 80.283 59.571
1.00 0.00 C<br /> HETATM 7595
N NIC 1 54.286 79.189 60.324
1.00 0.00 N<br /> HETATM 7596
C NIC 1 54.310 77.972 59.491
1.00 0.00 C<br /> HETATM 7597
H NIC 1 56.669 75.766 62.154
1.00 0.00 H<br /> HETATM 7598
H NIC 1 59.040 75.942 61.246
1.00 0.00 H<br /> HETATM 7599
H NIC 1 58.346 79.834 60.300
1.00 0.00 H<br /> HETATM 7600
H NIC 1 55.214 77.593 62.164
1.00 0.00 H<br /> HETATM 7601
H NIC 1 55.414 80.537 61.435
1.00 0.00 H<br /> HETATM 7602
H NIC 1 56.571 81.448 59.658
1.00 0.00 H<br /> HETATM 7603
H NIC 1 56.777 79.896 58.841
1.00 0.00 H<br /> HETATM 7604
H NIC 1 54.817 80.046 57.766
1.00 0.00 H<br /> HETATM 7605
H NIC 1 54.859 81.699 58.325
1.00 0.00 H<br /> HETATM 7606
H NIC 1 53.431 81.092 60.259
1.00 0.00 H<br /> HETATM 7607
H NIC 1 52.773 79.993 59.050
1.00 0.00 H<br /> HETATM 7608
H NIC 1 54.476 77.073 60.089
1.00 0.00 H<br /> HETATM 7609
H NIC 1 55.063 77.989 58.695
1.00 0.00 H<br /> HETATM 7610
H NIC 1 53.331 77.810 59.023
1.00 0.00 H</p><p _moz_di rty="" class="MsoNormal"><br _moz_dirty="" typ e="_moz" /></p><p _moz_dirty="" class="Mso Normal">Jaya.<br _moz_dirty="" /></p> </div>
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