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

[Justin A. Lemkul]

Read the documentation on the site where you got the ffamber ports:

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

The Amber force fields are particular about residue nomenclature.

-Justin

Quoting Liu Shiyong <liushiyong at gmail.com>:

> 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
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================