[gmx-users] amber force field problem: ignh doesnot work

[Liu Shiyong]

Hi,

I install amber  force filed according to source:

http://chemistry.csulb.edu/ffamber/index.html

But , I run pdb2gmx, I got a  problem.

Program pdb2gmx, VERSION 3.3.1

pdb2gmx -ignh -ff amber99 -f r-l_1.pdb


Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//ffamber99.rtp
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//aminoacids.dat
Reading r-l_1.pdb...
Read 3609 atoms
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 3 chains and 0 blocks of water and 449 residues with 3609 atoms

  chain  #res #atoms
  1 'A'   125   1006
  2 'B'   123    991
  3 'C'   201   1612

WARNING: there were 22 atoms with zero occupancy and 0 atoms with
         occupancy unequal to one (out of 3609 atoms). Check your pdb file.
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//ffamber99.atp
Atomtype 73
Reading residue database... (ffamber99)
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//ffamber99.rtp
Residue 132
Sorting it all out...
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//ffamber99.hdb
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//ffamber99-n.tdb
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//ffamber99-c.tdb
Processing chain 1 'A' (1006 atoms, 125 residues)
There are 184 donors and 188 acceptors
There are 306 hydrogen bonds
Will use HISB for residue 15
Will use HISA for residue 64
Will use HISB for residue 71
Will use HISB for residue 98
Will use HISB for residue 122
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Checking for duplicate atoms....
Now there are 1005 atoms. Deleted 1 duplicates.
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
                   CYS36   CYS78
                   SG297   SG627
   CYS78   SG627   1.318
  CYS112   SG896   0.969   1.027
N-terminus: none
C-terminus: none
Now there are 125 residues with 1842 atoms
Chain time...
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'HISA' not found in residue topology database, trying to use 'HID'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'
Warning: 'HISB' not found in residue topology database, trying to use 'HID'
Making bonds...
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//aminoacids.dat

WARNING: atom H is missing in residue ASP 1 in the pdb file
         You might need to add atom H to the hydrogen database of residue
ASP
         in the file ff???.hdb (see the manual)


WARNING: atom H is missing in residue LYSH 2 in the pdb file
         You might need to add atom H to the hydrogen database of residue
LYSH
         in the file ff???.hdb (see the manual)



WARNING: atom HB2 is missing in residue LYSH 2 in the pdb file
         You might need to add atom HB2 to the hydrogen database of residue
LYSH
         in the file ff???.hdb (see the manual)


WARNING: atom HG1 is missing in residue LYSH 2 in the pdb file
         You might need to add atom HG1 to the hydrogen database of residue
LYSH
         in the file ff???.hdb (see the manual)


-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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