AMBER Archive (2009)

Subject: Re: [AMBER] loadpdb

From: Jagdeesh C (jagc666_at_gmail.com)
Date: Tue Sep 08 2009 - 20:55:36 CDT

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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