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 <[email protected]> > On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım <[email protected]> > 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: SPC simple 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 list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet Yıldırım -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
