Re: [gmx-users] tip5p water model:Atomtype LP1 not found
I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL 512 commands: editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro topol.top after genbox command: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Fatal error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I got tip5p.gro from $GMXLIB 1.) editconf -f tip5p.gro -o protein.pdb 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 3 (TIP5P TIP 5-point) 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o protein-water.gro 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr Fatal error: number of coordinates in coordinate file (protein-water.gro, 37090) does not match topology (protein.top, 34530) What does the [molecules] directive of your .top say? In principle, most of the steps carried out above are unnecessary. You've got pure water, so the topology is easy: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL X ...where X is the number of water molecules. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On 4/15/13 6:58 AM, Ahmet yıldırım wrote: I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL 512 commands: editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro topol.top after genbox command: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Fatal error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. I cannot reproduce this problem with version 4.6, but it's trivial to just add the correct number of water molecules in the topology by hand. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] tip5p water model:Atomtype LP1 not found
I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 6:58 AM, Ahmet yıldırım wrote: I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL 512 commands: editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro topol.top after genbox command: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Fatal error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. I cannot reproduce this problem with version 4.6, but it's trivial to just add the correct number of water molecules in the topology by hand. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On 4/15/13 7:22 AM, Ahmet yıldırım wrote: I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? What exactly do you think is wrong? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] tip5p water model:Atomtype LP1 not found
The norm of force is very high. And the system converged in 3 steps For example, I got the following results for spc water model Steepest Descents converged to Fmax 1000 in 167 steps Potential Energy = -2.1208019e+05 Maximum force = 9.8452704e+02 on atom 286 Norm of force = 4.9830578e+01 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 7:22 AM, Ahmet yıldırım wrote: I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? What exactly do you think is wrong? -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On 4/15/13 8:28 AM, Ahmet yıldırım wrote: The norm of force is very high. And the system converged in 3 steps For example, I got the following results for spc water model Steepest Descents converged to Fmax 1000 in 167 steps Potential Energy = -2.1208019e+05 Maximum force = 9.8452704e+02 on atom 286 Norm of force = 4.9830578e+01 Fnorm is not particularly high here or in the previous post. The fact that it converged in 3 steps is also not unexpected. Minimizing a pure water system that is built from pre-equilibrated blocks should be easy. The potential is sensible and the maximum force is below your threshold. Everything is perfectly fine. -Justin 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 7:22 AM, Ahmet yıldırım wrote: I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? What exactly do you think is wrong? -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] tip5p water model:Atomtype LP1 not found
On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] tip5p water model:Atomtype LP1 not found
Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. How can you get it? 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. Is there going to be a protein in the system, as well? If so, gmx.ff is a poor choice and I would still maintain that despite any possible improvement in water model (and none of them are perfect), it's not a proper combination. If you're simulating pure water, the choice of parent force field is largely irrelevant. How can you get it? I have no idea why your tip5p.itp is wrong. The atom type should be MW for both LP1 and LP2, as I said before. Fix the atom types and the problem should go away. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] tip5p water model:Atomtype LP1 not found
I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. Is there going to be a protein in the system, as well? If so, gmx.ff is a poor choice and I would still maintain that despite any possible improvement in water model (and none of them are perfect), it's not a proper combination. If you're simulating pure water, the choice of parent force field is largely irrelevant. How can you get it? I have no idea why your tip5p.itp is wrong. The atom type should be MW for both LP1 and LP2, as I said before. Fix the atom types and the problem should go away. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? Well, they trigger a fatal error... Yes, they are wrong and newer versions of Gromacs are correct. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. Is there going to be a protein in the system, as well? If so, gmx.ff is a poor choice and I would still maintain that despite any possible improvement in water model (and none of them are perfect), it's not a proper combination. If you're simulating pure water, the choice of parent force field is largely irrelevant. How can you get it? I have no idea why your tip5p.itp is wrong. The atom type should be MW for both LP1 and LP2, as I said before. Fix the atom types and the problem should go away. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] tip5p water model:Atomtype LP1 not found
There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? Well, they trigger a fatal error... Yes, they are wrong and newer versions of Gromacs are correct. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. Is there going to be a protein in the system, as well? If so, gmx.ff is a poor choice and I would still maintain that despite any possible improvement in water model (and none of them are perfect), it's not a proper combination. If you're simulating pure water, the choice of parent force field is largely irrelevant. How can you get it? I have no idea why your tip5p.itp is wrong. The atom type should be MW for both LP1 and LP2, as I said before. Fix the atom types and the problem should go away. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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
Re: [gmx-users] tip5p water model:Atomtype LP1 not found
On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them They're there. The tip5p.gro file is in $GMXLIB and tip5p.itp is in several force field subdirectories. $ ls -l *.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber03.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber94.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber96.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99sb.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99sb-ildn.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amberGS.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 charmm27.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1434 Nov 27 20:24 oplsaa.ff/tip5p.itp -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? Well, they trigger a fatal error... Yes, they are wrong and newer versions of Gromacs are correct. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. Is there going to be a protein in the system, as well? If so, gmx.ff is a poor choice and I would still maintain that despite any possible improvement in water model (and none of them are perfect), it's not a proper combination. If you're simulating pure water, the choice of parent force field is largely irrelevant. How can you get it? I have no idea why your tip5p.itp is wrong. The atom type should be MW for both LP1 and LP2, as I said before. Fix the atom types and the problem should go away. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Ahmet Yıldırım -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist
Re: [gmx-users] tip5p water model:Atomtype LP1 not found
I am simulating tip5p water. I got tip5p.gro from $GMXLIB 1.) editconf -f tip5p.gro -o protein.pdb 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 3 (TIP5P TIP 5-point) 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o protein-water.gro 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr Fatal error: number of coordinates in coordinate file (protein-water.gro, 37090) does not match topology (protein.top, 34530) 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them They're there. The tip5p.gro file is in $GMXLIB and tip5p.itp is in several force field subdirectories. $ ls -l *.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber03.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber94.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber96.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99sb.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99sb-ildn.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amberGS.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 charmm27.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1434 Nov 27 20:24 oplsaa.ff/tip5p.itp -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? Well, they trigger a fatal error... Yes, they are wrong and newer versions of Gromacs are correct. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. Is there going to be a protein in the system, as well? If so, gmx.ff is a poor choice and I would still maintain that despite any possible improvement in water model (and none of them are perfect), it's not a proper combination. If you're simulating pure water, the choice of parent force field is largely irrelevant. How can you get it? I have no idea why your tip5p.itp is wrong. The atom type should be MW for both LP1 and LP2, as I said before. Fix the atom types and the problem should go away. -Justin 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 It looks like someone has erroneously modified your files. The TIP5P model should not be included in gmx.ff (Gromos force fields should be used with SPC), and the atom type for both LP1 and LP2 should be MW. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] tip5p water model:Atomtype LP1 not found
On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I got tip5p.gro from $GMXLIB 1.) editconf -f tip5p.gro -o protein.pdb 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 3 (TIP5P TIP 5-point) 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o protein-water.gro 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr Fatal error: number of coordinates in coordinate file (protein-water.gro, 37090) does not match topology (protein.top, 34530) What does the [molecules] directive of your .top say? In principle, most of the steps carried out above are unnecessary. You've got pure water, so the topology is easy: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL X ...where X is the number of water molecules. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] tip5p water model:Atomtype LP1 not found
Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 -- Ahmet Yıldırım -- 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
