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: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962
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