[gmx-users] #coordinates do not match
I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] #coordinates do not match
Hi, In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I don't think the ions are written into your .top . Please check and see if grompp works. On Sun, Aug 25, 2013 at 9:34 AM, The One And Only chappybo...@gmail.comwrote: I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] #coordinates do not match
How do you decrease the number of solvent molecules in a topology file? I think this will solve my problem. On Sat, Aug 24, 2013 at 9:08 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi, In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I don't think the ions are written into your .top . Please check and see if grompp works. On Sun, Aug 25, 2013 at 9:34 AM, The One And Only chappybo...@gmail.com wrote: I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
