AMBER Archive (2009)

Subject: Re: [AMBER] loadpdb

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Sep 09 2009 - 06:35:04 CDT

when you renamed the atoms it looks like you used the atom types, not
atom names.
for examples, "ca" is not an atom name, it is a type. also, the
residue names was "RES" and you changed it to parm99. I think you are
taking this information from the wrong place in the mol2 file. the
atom/residue names should not have changed in gaff- was there a
problem using the original PDB names and loading the gaff-generated
library files?

On Tue, Sep 8, 2009 at 9:55 PM, Jagdeesh C<jagc666_at_gmail.com> wrote:
> Hi All,
>
> I used autodock to dock my ligand on macromolecule. So i finally get a
> ligand docked structure. So I try to make a combine the pdbs. So I just
> paste my docked ligand pdb file with the initial macromolecule pdb file and
> I get a combined docked structure which seems to open well with VMD.
>
> This is how my combined pdb looks like
>
> 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
> ligand C
> ATOM      2  C2  RES d   1      -3.612  -4.112   3.429  0.00  0.00      p1
> ligand C
> ATOM      3  C3  RES d   1      -3.837  -3.526   4.664  0.00  0.00      p1
> ligand C
> ATOM      4  C4  RES d   1      -4.463  -2.296   4.718  0.00  0.00      p1
> ligand 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
> ligand C
> ATOM     36  C52 RES d   1      -6.820   3.764   7.573  0.00  0.00      p1
> ligand  C
> TER      37      RES d   1
> ATOM      1  C5' DG  1   4      -1.948  -4.520   9.025  1.00  0.17
> macro C
> ATOM      2  O5' DG  1   4      -2.353  -3.386   8.239  1.00  0.22
> macro O
> ATOM      3  C4' DG  1   4      -0.552  -5.028   8.668  1.00  0.14
> macro C
> ATOM      4  O4' DG  1   4      -0.492  -5.458   7.285  1.00  0.14
> macro  O
> ............................................ so on
>
> When I try loadpdb
>
>  $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
> -I: Adding /usr/local/bin/amber10/dat/leap/prep to search path.
> -I: Adding /usr/local/bin/amber10/dat/leap/lib to search path.
> -I: Adding /usr/local/bin/amber10/dat/leap/parm to search path.
> -I: Adding /usr/local/bin/amber10/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source /usr/local/bin/amber10//dat/leap/cmd/leaprc.ff99.
>
> Welcome to LEaP!
> Sourcing: /usr/local/bin/amber10//dat/leap/cmd/leaprc.ff99
> Log file: ./leap.log
> Loading parameters: /usr/local/bin/amber10/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading library: /usr/local/bin/amber10/dat/leap/lib/all_nucleic94.lib
> Loading library: /usr/local/bin/amber10/dat/leap/lib/all_amino94.lib
> Loading library: /usr/local/bin/amber10/dat/leap/lib/all_aminoct94.lib
> Loading library: /usr/local/bin/amber10/dat/leap/lib/all_aminont94.lib
> Loading library: /usr/local/bin/amber10/dat/leap/lib/ions94.lib
> Loading library: /usr/local/bin/amber10/dat/leap/lib/solvents.lib
>> souce leaprc.gaff
> ERROR: syntax error
>
>> source leaprc.gaff
> ----- Source: /usr/local/bin/amber10/dat/leap/cmd/leaprc.gaff
> ----- Source of /usr/local/bin/amber10/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /usr/local/bin/amber10/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic mol., add. info. at the end (June,
> 2003)
>> h3 = loadpdb xh3.pdb
> Loading PDB file: ./xh3.pdb
> Unknown residue: RES   number: 0   type: Terminal/last
> ..relaxing end constraints to try for a dbase match
>  -no luck
> Creating new UNIT for residue: RES sequence: 1
> Created a new atom named: C1 within residue: .R<RES 1>
> Created a new atom named: C2 within residue: .R<RES 1>
> Created a new atom named: C3 within residue: .R<RES 1>
> Created a new atom named: C4 within residue: .R<RES 1>
> Created a new atom named: C5 within residue: .R<RES 1>
> Created a new atom named: N6 within residue: .R<RES 1>
> Created a new atom named: C14 within residue: .R<RES 1>
> Created a new atom named: O15 within residue: .R<RES 1>
> Created a new atom named: N16 within residue: .R<RES 1>
> Created a new atom named: H17 within residue: .R<RES 1>
> Created a new atom named: C33 within residue: .R<RES 1>
> Created a new atom named: C34 within residue: .R<RES 1>
> Created a new atom named: C36 within residue: .R<RES 1>
> Created a new atom named: C39 within residue: .R<RES 1>
> Created a new atom named: C40 within residue: .R<RES 1>
> Created a new atom named: C41 within residue: .R<RES 1>
> Created a new atom named: N56 within residue: .R<RES 1>
> Created a new atom named: C44 within residue: .R<RES 1>
> Created a new atom named: C42 within residue: .R<RES 1>
> Created a new atom named: C35 within residue: .R<RES 1>
> Created a new atom named: C48 within residue: .R<RES 1>
> Created a new atom named: C10 within residue: .R<RES 1>
> Created a new atom named: O11 within residue: .R<RES 1>
> Created a new atom named: N12 within residue: .R<RES 1>
> Created a new atom named: H13 within residue: .R<RES 1>
> Created a new atom named: C18 within residue: .R<RES 1>
> Created a new atom named: C19 within residue: .R<RES 1>
> Created a new atom named: C21 within residue: .R<RES 1>
> Created a new atom named: C24 within residue: .R<RES 1>
> Created a new atom named: C25 within residue: .R<RES 1>
> Created a new atom named: C26 within residue: .R<RES 1>
> Created a new atom named: N57 within residue: .R<RES 1>
> Created a new atom named: C29 within residue: .R<RES 1>
> Created a new atom named: C27 within residue: .R<RES 1>
> Created a new atom named: C20 within residue: .R<RES 1>
> Created a new atom named: C52 within residue: .R<RES 1>
>  Added missing heavy atom: .R<DG 2>.A<C5' 5>
>  Added missing heavy atom: .R<DG 2>.A<P 1>
>  Added missing heavy atom: .R<DG 2>.A<O1P 2>
>  Added missing heavy atom: .R<DG 2>.A<O2P 3>
>  total atoms in file: 527
>  Leap added 193 missing atoms according to residue templates:
>       4 Heavy
>       189 H / lone pairs
>  The file contained 36 atoms not in residue templates
> check h3
> FATAL:  Atom .R<RES 1>.A<C1 1> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C2 2> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C3 3> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C4 4> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C5 5> does not have a type.
> FATAL:  Atom .R<RES 1>.A<N6 6> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C14 7> does not have a type.
> FATAL:  Atom .R<RES 1>.A<O15 8> does not have a type.
> FATAL:  Atom .R<RES 1>.A<N16 9> does not have a type.
> FATAL:  Atom .R<RES 1>.A<H17 10> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C33 11> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C34 12> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C36 13> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C39 14> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C40 15> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C41 16> does not have a type.
> FATAL:  Atom .R<RES 1>.A<N56 17> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C44 18> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C42 19> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C35 20> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C48 21> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C10 22> does not have a type.
> FATAL:  Atom .R<RES 1>.A<O11 23> does not have a type.
> FATAL:  Atom .R<RES 1>.A<N12 24> does not have a type.
> FATAL:  Atom .R<RES 1>.A<H13 25> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C18 26> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C19 27> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C21 28> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C24 29> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C25 30> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C26 31> does not have a type.
> FATAL:  Atom .R<RES 1>.A<N57 32> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C29 33> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C27 34> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C20 35> does not have a type.
> FATAL:  Atom .R<RES 1>.A<C52 36> does not have a type.
>
> So earlier I had used *antechamber* to make the *ligand* pdb into a mol2 ..
> This is the mol2 file
>
>  1 C1          1.2050    2.5210   -0.0810 ca        1 MOL      0.452928
>      2 C2          0.9330    3.8240    0.2960 ca        1 MOL     -0.452504
>      3 C3         -0.3870    4.2170    0.4480 ca        1 MOL      0.172723
>      4 C4         -1.3910    3.2970    0.2130 ca        1 MOL     -0.452504
>      5 C5         -1.0260    2.0250   -0.1790 ca        1 MOL      0.452928
>      6 N1          0.2330    1.6550   -0.3250 nb        1 MOL     -0.618666
>      7 C6          2.5910    2.0020   -0.3120 c         1 MOL      0.677044
>      8 O1          3.4270    2.6280   -0.9330 o         1 MOL     -0.535007
>      9 N2          2.8470    0.7680    0.2290 n         1 MOL     -0.809362
>     10 H1          2.0720    0.2390    0.5770 hn        1 MOL      0.345177
>     11 C7          4.0850    0.1100    0.2590 ca        1 MOL      0.435838
>     12 C8          4.5520   -0.5410   -0.8520 ca        1 MOL     -0.246793
>     13 C9          5.7810   -1.2170   -0.8410 ca        1 MOL      0.064011
>     14 C10         6.5470   -1.2270    0.3390 ca        1 MOL      0.231258
>     15 C11         6.2700   -1.8920   -1.9890 ca        1 MOL     -0.131737
>     16 C12         7.7790   -1.9070    0.3650 ca        1 MOL     -0.276913
>     17 N3          6.0460   -0.5610    1.4320 na        1 MOL     -0.037512
>     18 C13         8.2170   -2.5450   -0.7530 ca        1 MOL     -0.010035
>     19 C14         7.4590   -2.5410   -1.9450 ca        1 MOL     -0.143177
>     20 C15         4.8880    0.0760    1.4040 ca        1 MOL     -0.058325
>     21 C16         6.8300   -0.5460    2.7110 c3        1 MOL     -0.166681
>     22 C17        -2.0900    1.0200   -0.4680 c         1 MOL      0.677044
>     23 O2         -1.9010    0.0930   -1.2390 o         1 MOL     -0.535007
>     24 N4         -3.2500    1.2350    0.2050 n         1 MOL     -0.809362
>     25 H2         -3.2490    2.0390    0.8080 hn        1 MOL      0.345177
>     26 C18        -4.4030    0.4510    0.1420 ca        1 MOL      0.435838
>     27 C19        -4.3710   -0.8710    0.4960 ca        1 MOL     -0.246793
>     28 C20        -5.5240   -1.6700    0.4370 ca        1 MOL      0.064011
>     29 C21        -6.7330   -1.0980    0.0030 ca        1 MOL      0.231258
>     30 C22        -5.5010   -3.0390    0.8010 ca        1 MOL     -0.131737
> ................................. till 36
>
>
> So, I just renamed the capital letter atoms in my original pdb to
> small *corresponding
> to mol2* (in brown)  i got from antechamber .. as shown below
>
>
>
>
> ATOM      1  ca  parm99  1      -4.025  -3.449   2.287  0.00  0.00      p1
> ligand C
> ATOM      2  ca  parm99  1      -3.612  -4.112   3.429  0.00  0.00      p1
> ligand C
> ATOM      3  ca  parm99 1      -3.837  -3.526   4.664  0.00  0.00      p1
> ligand C
> ATOM      4  ca  parm99 1      -4.463  -2.296   4.718  0.00  0.00      p1
> ligand C
> ATOM      5  ca  parm99  1      -4.823  -1.699   3.526  0.00  0.00      p1
> C
> ATOM      6  nb  parm99 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
> .. here i have  renamed till 6 atoms to demonstrate .. in my pdb i did that
> for all 36 corresponding atoms
>
>
>
>
>
> Maybe the whole renaming procedure I am following is wrong. Basically, I
> just want to load my combined macro_ligand.pdb using loadpdb without any
> errors. I don't know if there is any standard way of doing that.
>
> Thank you very much for the earlier responses. I am again sorry, if I
> couldn't phrase my question well earlier.
>
>
> Regards,
> Jagdeesh
> _______________________________________________
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> AMBER_at_ambermd.org
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>

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