Hi,
I am sorry. I am pretty new to this so I couldnt phrase my question well.
Kindly disregard my previous question. I have this pdb file which I have
generated using autodock (ligand part)
REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.0
ATOM 1 C1 RES d 1 -4.025 -3.449 2.287 0.00 0.00 p1
C
ATOM 2 C2 RES d 1 -3.612 -4.112 3.429 0.00 0.00 p1
C
ATOM 3 C3 RES d 1 -3.837 -3.526 4.664 0.00 0.00 p1
C
ATOM 4 C4 RES d 1 -4.463 -2.296 4.718 0.00 0.00 p1
C
ATOM 5 C5 RES d 1 -4.823 -1.699 3.526 0.00 0.00 p1
C
ATOM 6 N6 RES d 1 -4.605 -2.259 2.351 0.00 0.00 p1
N
ATOM 7 C14 RES d 1 -3.797 -3.971 0.902 0.00 0.00 p1
C
ATOM 8 O15 RES d 1 -2.736 -4.447 0.551 0.00 0.00 p1
O
ATOM 9 N16 RES d 1 -4.875 -3.872 0.059 0.00 0.00 p1
N
ATOM 10 H17 RES d 1 -5.654 -3.321 0.358 0.00 0.00 p1
H
ATOM 11 C33 RES d 1 -4.966 -4.386 -1.243 0.00 0.00 p1
C
ATOM 12 C34 RES d 1 -4.383 -3.726 -2.292 0.00 0.00 p1
C
ATOM 13 C36 RES d 1 -4.473 -4.214 -3.604 0.00 0.00 p1
C
ATOM 14 C39 RES d 1 -5.181 -5.406 -3.844 0.00 0.00 p1
C
ATOM 15 C40 RES d 1 -3.871 -3.535 -4.694 0.00 0.00 p1
C
ATOM 16 C41 RES d 1 -5.284 -5.903 -5.157 0.00 0.00 p1
C
ATOM 17 N56 RES d 1 -5.750 -6.040 -2.766 0.00 0.00 p1
N
ATOM 18 C44 RES d 1 -4.695 -5.226 -6.179 0.00 0.00 p1
C
ATOM 19 C42 RES d 1 -3.980 -4.029 -5.951 0.00 0.00 p1
C
ATOM 20 C35 RES d 1 -5.651 -5.570 -1.534 0.00 0.00 p1
C
ATOM 21 C48 RES d 1 -6.513 -7.314 -2.977 0.00 0.00 p1
C
ATOM 22 C10 RES d 1 -5.474 -0.357 3.553 0.00 0.00 p1
C
ATOM 23 O11 RES d 1 -5.386 0.415 2.612 0.00 0.00 p1
O
ATOM 24 N12 RES d 1 -6.160 -0.099 4.696 0.00 0.00 p1
N
ATOM 25 H13 RES d 1 -6.144 -0.837 5.378 0.00 0.00 p1
H
ATOM 26 C18 RES d 1 -6.876 1.063 4.989 0.00 0.00 p1
C
ATOM 27 C19 RES d 1 -7.921 1.460 4.199 0.00 0.00 p1
C
ATOM 28 C21 RES d 1 -8.648 2.627 4.484 0.00 0.00 p1
C
ATOM 29 C24 RES d 1 -8.292 3.401 5.603 0.00 0.00 p1
C
ATOM 30 C25 RES d 1 -9.731 3.047 3.672 0.00 0.00 p1
C
ATOM 31 C26 RES d 1 -9.013 4.574 5.899 0.00 0.00 p1
C
ATOM 32 N57 RES d 1 -7.236 2.969 6.370 0.00 0.00 p1
N
ATOM 33 C29 RES d 1 -10.047 4.946 5.099 0.00 0.00 p1
C
ATOM 34 C27 RES d 1 -10.414 4.178 3.972 0.00 0.00 p1
C
ATOM 35 C20 RES d 1 -6.562 1.868 6.090 0.00 0.00 p1
C
ATOM 36 C52 RES d 1 -6.820 3.764 7.573 0.00 0.00 p1
C
TER 37
I want to add it to my macromolecule pdb. So I add the text file at front of
my macromolecule pdb file. So now I have ligand + macromolecule pdb file
which opens well with VMD the whole structure.
When i tried my loadpdb
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
>source leaprc
mypdb = loadpdb ligand_macro.pdb
I get
The file contained 36 atoms not in residue templates for all the above atoms
(FATAL: Atom .R<RES>.A<xxx> does not have a type) for all of them.
So I tried renaming the pdb ligand part as below and now it says 11 atoms
not in residue templates as shown in my previous question.
How do I fix my error, or what basic mistake am I making? Kindly let me know
if I need to give more information.
Regards,
Jagdeesh
On Mon, Sep 7, 2009 at 11:31 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> How did you generate the pdb file?
>
>
> On Sep 7, 2009, at 1:36 PM, Jagdeesh C <jagc666.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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Received on Mon Sep 14 2009 - 13:31:16 PDT
