AMBER Archive (2009)

Subject: Re: [AMBER] loadpdb

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 07 2009 - 13:01:10 CDT

How did you generate the pdb file?

On Sep 7, 2009, at 1:36 PM, Jagdeesh C <jagc666_at_gmail.com> wrote:

> Hello Amber Users,
>
> I have this pdb file
>
> ATOM 1 ca parm99 3 1.205 2.521 -0.081
> ATOM 2 ca parm99 3 0.933 3.824 0.296
> ATOM 3 ca parm99 3 -0.387 4.217 0.448
> ATOM 4 ca parm99 3 -1.391 3.297 0.213
> ATOM 5 ca parm99 3 -1.026 2.025 -0.179
> ATOM 6 nb parm99 3 0.233 1.655 -0.325
> ATOM 7 c parm99 3 2.591 2.002 -0.312
> ATOM 8 o parm99 3 3.427 2.628 -0.933
> ATOM 9 n parm99 3 2.847 0.768 0.229
> ATOM 10 hn parm99 3 2.072 0.239 0.577
> ATOM 11 ca parm99 3 4.085 0.110 0.259
> ATOM 12 ca parm99 3 4.552 -0.541 -0.852
> ATOM 13 ca parm99 3 5.781 -1.217 -0.841
> ATOM 14 ca parm99 3 6.547 -1.227 0.339
> ATOM 15 ca parm99 3 6.270 -1.892 -1.989
> ATOM 16 ca parm99 3 7.779 -1.907 0.365
> ATOM 17 na parm99 3 6.046 -0.561 1.432
> ATOM 18 ca parm99 3 8.217 -2.545 -0.753
> ATOM 19 ca parm99 3 7.459 -2.541 -1.945
> ATOM 20 ca parm99 3 4.888 0.076 1.404
> ATOM 21 c3 parm99 3 6.830 -0.546 2.711
> ATOM 22 c parm99 3 -2.090 1.020 -0.468
> ATOM 23 o parm99 3 -1.901 0.093 -1.239
> ATOM 24 n parm99 3 -3.250 1.235 0.205
> ATOM 25 hn parm99 3 -3.249 2.039 0.808
> ATOM 26 ca parm99 3 -4.403 0.451 0.142
> ATOM 27 ca parm99 3 -4.371 -0.871 0.496
> ATOM 28 ca parm99 3 -5.524 -1.670 0.437
> ATOM 29 ca parm99 3 -6.733 -1.098 0.003
> ATOM 30 ca parm99 3 -5.501 -3.039 0.801
> ATOM 31 ca parm99 3 -7.897 -1.889 -0.061
> ATOM 32 na parm99 3 -6.723 0.232 -0.345
> ATOM 33 ca parm99 3 -7.838 -3.199 0.297
> ATOM 34 ca parm99 3 -6.630 -3.785 0.733
> ATOM 35 ca parm99 3 -5.630 0.972 -0.283
> ATOM 36 c3 parm99 3 -7.991 0.885 -0.814
> ATOM 37 ha parm99 3 1.729 4.518 0.469
> ATOM 38 ha parm99 3 -0.625 5.218 0.742
> ATOM 39 ha parm99 3 -2.421 3.563 0.332
> ATOM 40 ha parm99 3 3.967 -0.534 -1.748
> ATOM 41 ha parm99 3 5.697 -1.889 -2.893
> ATOM 42 ha parm99 3 8.367 -1.922 1.259
> ATOM 43 ha parm99 3 9.155 -3.060 -0.730
> ATOM 44 ha parm99 3 7.823 -3.050 -2.813
> ATOM 45 h4 parm99 3 4.554 0.583 2.285
> ATOM 46 h1 parm99 3 6.296 0.013 3.450
> ATOM 47 h1 parm99 3 7.783 -0.091 2.539
> ATOM 48 h1 parm99 3 6.970 -1.550 3.055
> ATOM 49 ha parm99 3 -3.449 -1.304 0.825
> ATOM 50 ha parm99 3 -4.587 -3.487 1.131
> ATOM 51 ha parm99 3 -8.821 -1.461 -0.390
> ATOM 52 ha parm99 3 -8.724 -3.796 0.247
> ATOM 53 ha parm99 3 -6.606 -4.819 1.010
> ATOM 54 h4 parm99 3 -5.685 2.002 -0.566
> ATOM 55 h1 parm99 3 -7.800 1.913 -1.040
> ATOM 56 h1 parm99 3 -8.731 0.820 -0.045
> ATOM 57 h1 parm99 3 -8.344 0.386 -1.692
> TER 58 parm99 3
> ATOM 1 C5' DG 1 4 -1.948 -4.520 9.025 1.00
> 0.17 2HY9
> C
> ATOM 2 O5' DG 1 4 -2.353 -3.386 8.239 1.00
> 0.22 2HY9
> O
> .........................
>
> this is a part of organic ligand
>
> when i loadpdb i get the following error
>
>> h3 = loadpdb h3.pdb
> Loading PDB file: ./h3.pdb
> -- residue 9: duplicate [ c] atoms (total 2)
> -- residue 9: duplicate [ c3] atoms (total 2)
> -- residue 9: duplicate [ ca] atoms (total 23)
> -- residue 9: duplicate [ h1] atoms (total 6)
> -- residue 9: duplicate [ h4] atoms (total 2)
> -- residue 9: duplicate [ ha] atoms (total 13)
> -- residue 9: duplicate [ hn] atoms (total 2)
> -- residue 9: duplicate [ n] atoms (total 2)
> -- residue 9: duplicate [ na] atoms (total 2)
> -- residue 9: duplicate [ o] 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.)
>
> Unknown residue: par number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: par sequence: 9
> Created a new atom named: ca within residue: .R<par 9>
> Created a new atom named: nb within residue: .R<par 9>
> Created a new atom named: c within residue: .R<par 9>
> Created a new atom named: o within residue: .R<par 9>
> Created a new atom named: n within residue: .R<par 9>
> Created a new atom named: hn within residue: .R<par 9>
> Created a new atom named: na within residue: .R<par 9>
> Created a new atom named: c3 within residue: .R<par 9>
> Created a new atom named: ha within residue: .R<par 9>
> Created a new atom named: h4 within residue: .R<par 9>
> Created a new atom named: h1 within residue: .R<par 9>
> Added missing heavy atom: .R<DG 10>.A<P 1>
> Added missing heavy atom: .R<DG 10>.A<O1P 2>
> Added missing heavy atom: .R<DG 10>.A<O2P 3>
> total atoms in file: 549
> Leap added 192 missing atoms according to residue templates:
> 3 Heavy
> 189 H / lone pairs
> The file contained 11 atoms not in residue templates
>> check h3
> Checking 'h3'....
> WARNING: The unperturbed charge of the unit: -21.000000 is not zero.
> FATAL: Atom .R<par 9>.A<ca 1> does not have a type.
> FATAL: Atom .R<par 9>.A<nb 2> does not have a type.
> FATAL: Atom .R<par 9>.A<c 3> does not have a type.
> FATAL: Atom .R<par 9>.A<o 4> does not have a type.
> FATAL: Atom .R<par 9>.A<n 5> does not have a type.
> FATAL: Atom .R<par 9>.A<hn 6> does not have a type.
> FATAL: Atom .R<par 9>.A<na 7> does not have a type.
> FATAL: Atom .R<par 9>.A<c3 8> does not have a type.
> FATAL: Atom .R<par 9>.A<ha 9> does not have a type.
> FATAL: Atom .R<par 9>.A<h4 10> does not have a type.
> FATAL: Atom .R<par 9>.A<h1 11> does not have a type.
> Warning: Close contact of 0.767630 angstroms between .R<par 9>.A<nb
> 2> and
> .R<DG 29>.A<C4 27>
> Warning: Close contact of 0.293156 angstroms between .R<par 9>.A<nb
> 2> and
> .R<DG 29>.A<N3 26>
> Warning: Close contact of 2.021928 angstroms between .R<par 9>.A<nb
> 2> and
> .R<DG 29>.A<C2 22>
> Warning: Close contact of 0.929842 angstroms between .R<par 9>.A<o
> 4> and
> .R<DG 28>.A<O6 19>
> Warning: Close contact of 2.057501 angstroms between .R<par 9>.A<o
> 4> and
> .R<DG 28>.A<C6 18>
> Warning: Close contact of 1.904166 angstroms between .R<par 9>.A<n
> 5> and
> .R<DG 10>.A<H21 24>
> Warning: Close contact of 1.067867 angstroms between .R<par 9>.A<hn
> 6> and
> .R<DG 29>.A<H5'2 7>
> Warning: Close contact of 1.989053 angstroms between .R<par 9>.A<na
> 7> and
> .R<DA 27>.A<H1' 12>
> Warning: Close contact of 0.770428 angstroms between .R<par 9>.A<h4
> 10> and
> .R<DG 28>.A<H5'1 6>
> Warning: Close contact of 1.821572 angstroms between .R<DG
> 22>.A<H2'2 32>
> and .R<DG 23>.A<H5'1 6>
> Warning: Close contact of 1.754674 angstroms between .R<DT
> 25>.A<H2'1 30>
> and .R<DA 27>.A<H62 21>
> Checking parameters for unit 'h3'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 11 Warnings: 12
>>
>
>
> How can I fix this problem. I would really appreciate any help.
> Thank you.
>
> Regards,
> Jagdeesh
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