AMBER Archive (2009)

Subject: Re: [AMBER] xleap not reconizing inhibitor prepin

From: Junmei Wang (junmwang_at_gmail.com)
Date: Mon Oct 26 2009 - 09:51:41 CDT

The problem is the atom names of your input pdb do not match the atom names
in the prepin file. Therefore, you need to manually modify the atoms of the
ligand in your pdb file. There are some ways to handle such kind of atom
name mismatch problem, you may search the archive or find them in the
manual.

Best

Junmei

On Fri, Oct 23, 2009 at 11:21 AM, Jayalakshmi Sridhar <jsridhar_at_xula.edu>wrote:

>
> Dear Amber Users,
> I am resending my earlier mail as it is not going through properly. Sorry
> about the multiple emails.
> Jaya
>
>
> ---------- Forwarded message ----------
> From: Jayalakshmi sridhar <jaya_sri1969_at_yahoo.com>
> To: jsridhar_at_xula.edu
> Date: Fri, 23 Oct 2009 09:18:04 -0700 (PDT)
> Subject: amber
>
> Dear Amber Users,
> I have a protein with a small molecule docked in it. I need to minimize
> the
> complex. I ran the inhibitor through antechamber to generate prepin and
> frcmod files. I then loaded the prepin file in xleap and then the complex
> pdb file. All help is greatly appreciated. Thanks.
> This is the output I am getting in xleap:
> 1z10nic = loadpdb 1z10nic_mod5.pdb
> Loading PDB file: ./1z10nic_mod5.pdb
> -- residue 495: duplicate [ C] atoms (total 10)
> -- residue 495: duplicate [ H] atoms (total 14)
> -- residue 495: duplicate [ N] atoms (total 2)
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
> One sided connection. Residue: missing connect0 atom.
> One sided connection. Residue: missing connect1 atom.
> Added missing heavy atom: .R<CARG 494>.A<OXT 25>
> Added missing heavy atom: .R<NIC 495>.A<C1 4>
> Added missing heavy atom: .R<NIC 495>.A<C4 8>
> Added missing heavy atom: .R<NIC 495>.A<C3 10>
> Added missing heavy atom: .R<NIC 495>.A<C5 11>
> Added missing heavy atom: .R<NIC 495>.A<C2 1>
> Added missing heavy atom: .R<NIC 495>.A<C6 13>
> Added missing heavy atom: .R<NIC 495>.A<N1 22>
> Added missing heavy atom: .R<NIC 495>.A<C7 16>
> Added missing heavy atom: .R<NIC 495>.A<C8 19>
> Added missing heavy atom: .R<NIC 495>.A<C9 23>
> This is my .prepin file:
> 0 0 2
> This is a remark line
> molecule.res
> NIC INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 C2 ca M 3 2 1 1.540 111.208 180.000 0.398300
> 5 H2 h4 E 4 3 2 1.082 110.285 152.021 0.023500
> 6 N nb M 4 3 2 1.338 132.082 -5.372 -0.667400
> 7 C1 ca M 6 4 3 1.334 114.508 -15.311 0.393700
> 8 H1 h4 E 7 6 4 1.081 115.704 171.419 0.022000
> 9 C ca M 7 6 4 1.378 122.650 -9.218 -0.249500
> 10 H ha E 9 7 6 1.057 124.491 -179.429 0.143600
> 11 C4 ca M 9 7 6 1.358 121.446 3.759 -0.084900
> 12 H3 ha E 11 9 7 1.086 120.269 177.462 0.150100
> 13 C3 ca M 11 9 7 1.362 116.419 8.515 -0.193500
> 14 C5 c3 M 13 11 9 1.475 118.393 156.894 0.210100
> 15 H4 h1 E 14 13 11 1.089 110.042 90.624 0.068300
> 16 C6 c3 M 14 13 11 1.506 110.030 -150.548 -0.101800
> 17 H5 hc E 16 14 13 1.094 112.449 -93.517 0.055800
> 18 H6 hc E 16 14 13 1.089 112.965 29.014 0.047000
> 19 C7 c3 M 16 14 13 1.480 102.822 145.879 -0.102500
> 20 H7 hc E 19 16 14 1.092 111.815 -110.001 0.047800
> 21 H8 hc E 19 16 14 1.074 105.271 133.653 0.049600
> 22 C8 c3 M 19 16 14 1.519 106.734 9.135 0.147400
> 23 H9 h1 E 22 19 16 1.093 111.474 80.768 0.055700
> 24 H10 h1 E 22 19 16 1.095 114.538 -157.270 0.044700
> 25 N1 n3 M 22 19 16 1.455 101.442 -35.278 -0.704200
> 26 C9 c3 M 25 22 19 1.475 109.554 -77.222 0.141400
> 27 H11 h1 E 26 25 22 1.092 111.860 -163.695 0.049300
> 28 H12 h1 E 26 25 22 1.096 114.117 73.566 0.011700
> 29 H13 h1 E 26 25 22 1.097 110.378 -47.999 0.043800
> LOOP
> C3 C2
> N1 C5
> IMPROPER
> C3 H2 C2 N
> C H1 C1 N
> C4 C1 C H
> C3 C C4 H3
> C4 C1 C H
> C3 C C4 H3
> C5 C4 C3 C2
> DONE
> STOP
> This is the HETATM in pdb file:
> HETATM 7585 C NIC 1 57.090 76.668 61.797 1.00 0.00
> C
> HETATM 7586 C NIC 1 58.370 76.789 61.300 1.00 0.00
> C
> HETATM 7587 N NIC 1 58.868 77.949 60.869 1.00 0.00
> N
> HETATM 7588 C NIC 1 57.971 78.938 60.776 1.00 0.00
> C
> HETATM 7589 C NIC 1 56.635 78.838 61.141 1.00 0.00
> C
> HETATM 7590 C NIC 1 56.231 77.720 61.806 1.00 0.00
> C
> HETATM 7591 C NIC 1 55.606 79.785 60.671 1.00 0.00
> C
> HETATM 7592 C NIC 1 56.085 80.494 59.432 1.00 0.00
> C
> HETATM 7593 C NIC 1 54.838 80.678 58.656 1.00 0.00
> C
> HETATM 7594 C NIC 1 53.691 80.283 59.571 1.00 0.00
> C
> HETATM 7595 N NIC 1 54.286 79.189 60.324 1.00 0.00
> N
> HETATM 7596 C NIC 1 54.310 77.972 59.491 1.00 0.00
> C
> HETATM 7597 H NIC 1 56.669 75.766 62.154 1.00 0.00
> H
> HETATM 7598 H NIC 1 59.040 75.942 61.246 1.00 0.00
> H
> HETATM 7599 H NIC 1 58.346 79.834 60.300 1.00 0.00
> H
> HETATM 7600 H NIC 1 55.214 77.593 62.164 1.00 0.00
> H
> HETATM 7601 H NIC 1 55.414 80.537 61.435 1.00 0.00
> H
> HETATM 7602 H NIC 1 56.571 81.448 59.658 1.00 0.00
> H
> HETATM 7603 H NIC 1 56.777 79.896 58.841 1.00 0.00
> H
> HETATM 7604 H NIC 1 54.817 80.046 57.766 1.00 0.00
> H
> HETATM 7605 H NIC 1 54.859 81.699 58.325 1.00 0.00
> H
> HETATM 7606 H NIC 1 53.431 81.092 60.259 1.00 0.00
> H
> HETATM 7607 H NIC 1 52.773 79.993 59.050 1.00 0.00
> H
> HETATM 7608 H NIC 1 54.476 77.073 60.089 1.00 0.00
> H
> HETATM 7609 H NIC 1 55.063 77.989 58.695 1.00 0.00
> H
> HETATM 7610 H NIC 1 53.331 77.810 59.023 1.00 0.00
> H
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber