Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers
Thank you for your reply. I am just wondering is there anyway we can make pdb2gmx change the default digit number? I am doing a membrane protein, and I already have a ideal model as a pdb file. If I need to go over the solvate(or genbox in the 4.5.x version), by default waterbox setting the water will go into the lipid layer since the algorithm is just to put water into all the spaces, I may have to manually delete those water. If I can just transfer the model it will make life much easier and I can also compare with the known result. Thanks again for your time! In addition to what Joao said, the fixed-width .pdb format is fundamentally unsuited to large systems. You need to find a way to avoid using such a .pdb file as input to pdb2gmx; either solvate later, or use a different format for input. Mark On Mon, Aug 4, 2014 at 11:09 PM, WH signoreguid...@163.com wrote: Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers
Is there a specific reason why you're not adding the water using genbox and genion? If that's not the case you can simply delete the waters from the pdb and only convert the rest of the system. Then you can solvate, set your box boundaries and add ions. Best, João *Joao Martins* joaomartins...@gmail.com On Tue, Aug 5, 2014 at 6:09 AM, WH signoreguid...@163.com wrote: Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers
In addition to what Joao said, the fixed-width .pdb format is fundamentally unsuited to large systems. You need to find a way to avoid using such a .pdb file as input to pdb2gmx; either solvate later, or use a different format for input. Mark On Mon, Aug 4, 2014 at 11:09 PM, WH signoreguid...@163.com wrote: Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx cannot generate the right residue and atom numbers
Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
