<br>Hi,<br><br>I install amber force filed according to source:<br><br><a href="http://chemistry.csulb.edu/ffamber/index.html">http://chemistry.csulb.edu/ffamber/index.html</a><br><br>But , I run pdb2gmx, I got a problem.<br>
<br>Program pdb2gmx, VERSION 3.3.1<br><br>pdb2gmx -ignh -ff amber99 -f r-l_1.pdb <br clear="all"><br><br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//ffamber99.rtp<br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//aminoacids.dat<br>
Reading r-l_1.pdb...<br>Read 3609 atoms<br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//xlateat.dat<br>26 out of 26 lines of xlateat.dat converted succesfully<br>Analyzing pdb file<br>There are 3 chains and 0 blocks of water and 449 residues with 3609 atoms<br>
<br> chain #res #atoms<br> 1 'A' 125 1006<br> 2 'B' 123 991<br> 3 'C' 201 1612<br><br>WARNING: there were 22 atoms with zero occupancy and 0 atoms with<br> occupancy unequal to one (out of 3609 atoms). Check your pdb file.<br>
Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//ffamber99.atp<br>Atomtype 73<br>Reading residue database... (ffamber99)<br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//ffamber99.rtp<br>
Residue 132<br>Sorting it all out...<br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//ffamber99.hdb<br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//ffamber99-n.tdb<br>
Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//ffamber99-c.tdb<br>Processing chain 1 'A' (1006 atoms, 125 residues)<br>There are 184 donors and 188 acceptors<br>There are 306 hydrogen bonds<br>
Will use HISB for residue 15<br>Will use HISA for residue 64<br>Will use HISB for residue 71<br>Will use HISB for residue 98<br>Will use HISB for residue 122<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>
Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>
Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br> Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>
Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>Checking for duplicate atoms....<br>Now there are 1005 atoms. Deleted 1 duplicates.<br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//specbond.dat<br>
5 out of 5 lines of specbond.dat converted succesfully<br>Special Atom Distance matrix:<br> CYS36 CYS78<br> SG297 SG627<br> CYS78 SG627 1.318<br> CYS112 SG896 0.969 1.027<br>
N-terminus: none<br>C-terminus: none<br>Now there are 125 residues with 1842 atoms<br>Chain time...<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>
Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>
Warning: 'HISA' not found in residue topology database, trying to use 'HID'<br>Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>
Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>Warning: 'LYSH' not found in residue topology database, trying to use 'LYN'<br>Warning: 'HISB' not found in residue topology database, trying to use 'HID'<br>
Making bonds...<br>Opening library file /export/apps/gromacs-3.3.1-Amber/share/gromacs/top//aminoacids.dat<br><br>WARNING: atom H is missing in residue ASP 1 in the pdb file<br> You might need to add atom H to the hydrogen database of residue ASP<br>
in the file ff???.hdb (see the manual)<br><br><br>WARNING: atom H is missing in residue LYSH 2 in the pdb file<br> You might need to add atom H to the hydrogen database of residue LYSH<br> in the file ff???.hdb (see the manual)<br>
<br><br><br>WARNING: atom HB2 is missing in residue LYSH 2 in the pdb file<br> You might need to add atom HB2 to the hydrogen database of residue LYSH<br> in the file ff???.hdb (see the manual)<br><br><br>
WARNING: atom HG1 is missing in residue LYSH 2 in the pdb file<br> You might need to add atom HG1 to the hydrogen database of residue LYSH<br> in the file ff???.hdb (see the manual)<br><br><br>-- <br>Shiyong Liu<br>
Research Assistant<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone: (785) 864-1962