AMBER Archive (2009)

Subject: [AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure

From: Yunjie Zhao (yjzhao.wh_at_gmail.com)
Date: Thu Nov 19 2009 - 22:37:34 CST

Dear Amber Users:

    I would like to simulate the RNA with one seperate Adenine molecule. The
end of the PDB file is like this
ATOM 1663 N6 A A 52 7.335 -39.271 -8.372
ATOM 1664 1H6 A A 52 8.259 -39.198 -8.763
ATOM 1665 2H6 A A 52 7.171 -39.494 -7.402
ATOM 1666 N1 A A 52 6.687 -38.594 -10.376
ATOM 1667 C2 A A 52 5.735 -38.244 -11.232
ATOM 1668 H2 A A 52 6.068 -37.953 -12.220
ATOM 1669 N3 A A 52 4.420 -38.215 -11.027
ATOM 1670 C4 A A 52 4.088 -38.591 -9.759
ATOM 1671 C3* A A 52 0.164 -40.291 -9.764
ATOM 1672 H3* A A 52 0.750 -40.807 -9.000
ATOM 1673 C2* A A 52 1.115 -39.617 -10.762
ATOM 1674 O2* A A 52 0.455 -39.176 -11.950
ATOM 1675 O3* A A 52 -0.743 -41.197 -10.394
ATOM 1676 1H2* A A 52 2.144 -39.887 -10.524
ATOM 1677 2HO* A A 52 0.168 -39.938 -12.458
TER 1678 A A 52
HETATM 1785 N SAM A 100 12.696 -24.660 -6.470
HETATM 1786 CA SAM A 100 12.595 -24.516 -7.944
HETATM 1787 C SAM A 100 13.570 -25.465 -8.638
HETATM 1788 O SAM A 100 13.603 -25.525 -9.863
HETATM 1789 OXT SAM A 100 14.369 -26.124 -7.987
HETATM 1790 CB SAM A 100 12.939 -23.070 -8.357
HETATM 1791 CG SAM A 100 11.744 -22.108 -8.225
HETATM 1792 SD SAM A 100 12.360 -20.499 -7.622
HETATM 1793 CE SAM A 100 11.525 -20.478 -6.014
HETATM 1794 C5' SAM A 100 11.311 -19.312 -8.509
HETATM 1795 C4' SAM A 100 11.747 -17.912 -8.087
HETATM 1796 O4' SAM A 100 13.137 -17.816 -8.299
HETATM 1797 C3' SAM A 100 11.098 -16.828 -8.955
HETATM 1798 O3' SAM A 100 10.014 -16.175 -8.283
HETATM 1799 C2' SAM A 100 12.263 -15.830 -9.229
HETATM 1800 O2' SAM A 100 11.796 -14.495 -8.999
HETATM 1801 C1' SAM A 100 13.442 -16.433 -8.389
HETATM 1802 N9 SAM A 100 14.759 -16.258 -9.017
HETATM 1803 C8 SAM A 100 15.137 -16.676 -10.268
HETATM 1804 N7 SAM A 100 16.385 -16.353 -10.497
HETATM 1805 C5 SAM A 100 16.890 -15.715 -9.416
HETATM 1806 C6 SAM A 100 18.143 -15.142 -9.074
HETATM 1807 N6 SAM A 100 19.186 -15.167 -9.964
HETATM 1808 N1 SAM A 100 18.297 -14.572 -7.865
HETATM 1809 C2 SAM A 100 17.305 -14.544 -6.977
HETATM 1810 N3 SAM A 100 16.100 -15.050 -7.262
HETATM 1811 C4 SAM A 100 15.852 -15.646 -8.447
There are 27 SAM atoms at the end of the pdb file
When I use the tleap with leap.rna.ff98 force field, some errors happened
> model=loadpdb sam_5.pdb
Loading PDB file: ./sam_5.pdb
Unknown residue: SAM number: 52 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Created a new atom named: P within residue: .R<RG5 1>
Created a new atom named: O1P within residue: .R<RG5 1>
Created a new atom named: O2P within residue: .R<RG5 1>
Creating new UNIT for residue: SAM sequence: 53
Created a new atom named: N within residue: .R<SAM 53>
Created a new atom named: CA within residue: .R<SAM 53>
Created a new atom named: C within residue: .R<SAM 53>
Created a new atom named: O within residue: .R<SAM 53>
Created a new atom named: OXT within residue: .R<SAM 53>
Created a new atom named: CB within residue: .R<SAM 53>
Created a new atom named: CG within residue: .R<SAM 53>
Created a new atom named: SD within residue: .R<SAM 53>
Created a new atom named: CE within residue: .R<SAM 53>
Created a new atom named: C5' within residue: .R<SAM 53>
Created a new atom named: C4' within residue: .R<SAM 53>
Created a new atom named: O4' within residue: .R<SAM 53>
Created a new atom named: C3' within residue: .R<SAM 53>
Created a new atom named: O3' within residue: .R<SAM 53>
Created a new atom named: C2' within residue: .R<SAM 53>
Created a new atom named: O2' within residue: .R<SAM 53>
Created a new atom named: C1' within residue: .R<SAM 53>
Created a new atom named: N9 within residue: .R<SAM 53>
Created a new atom named: C8 within residue: .R<SAM 53>
Created a new atom named: N7 within residue: .R<SAM 53>
Created a new atom named: C5 within residue: .R<SAM 53>
Created a new atom named: C6 within residue: .R<SAM 53>
Created a new atom named: N6 within residue: .R<SAM 53>
Created a new atom named: N1 within residue: .R<SAM 53>
Created a new atom named: C2 within residue: .R<SAM 53>
Created a new atom named: N3 within residue: .R<SAM 53>
Created a new atom named: C4 within residue: .R<SAM 53>
  total atoms in file: 1704
  Leap added 2 missing atoms according to residue templates:
       2 H / lone pairs
  The file contained 30 atoms not in residue templates
>

It adds many extral atoms what I don't want, and I couldn't save the top and
crd files.

I want ot use Antechamber to Create Leap Input Files for Simulating using
the General Amber Force Field. But it did not work.

$ $AMBERHOME/exe/antechamber -i sam.pdb -fi pdb -o sam.mol2 -fo mol2 -c bcc
-s 2
Running: /export/home/***/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0
-o ANTECHAMBER_BOND_TYPE.AC <http://antechamber_bond_type.ac/> -f ac -j full
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly
increase the computer time
Error: cannot run "/export/home/zyj/amber9/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC<http://antechamber_bond_type.ac/>-f ac -j
full" in judgebondtype() of antechamber.c properly, exit

If I use Xleap to creat the Non-Standard molecule, it needs to specify the
atom types and charges. But I do not know how to obtain and use R.E.D
available at http://www.u-picardie.fr/labo/lbpd/RED/.

Please help me out!

Thanks for your patient and help 

-- 
Yunjie Zhao
------------------------------------------------------------------
Department of Physics,
Huazhong University of Science and Technology,
Wuhan 430074, Hubei, China
------------------------------------------------------------------
  • chemical/x-pdb attachment: sam.pdb

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