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 <[EMAIL PROTECTED]>: > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
