[gmx-users] Atomype HW not found

2011-01-09 Thread trevor brown
Dear all, I have "Atomype HW not found" error when I use gromos43a1 in water at the end of grompp. However there is no error if I just change the forcefield to oplsaa. My topology file follows. Any suggestions? trevor ; Include forcefield parameters #include "gromos43a1.ff/forcefield.itp" [ mol

[gmx-users] Atomtpe HW not found-2

2011-01-09 Thread trevor brown
Dear friends, My run commands are below. It works without any error. However if I add -water tip3p at the end of pdg2gmx ... line it causes an error (Atomtpe HW not found) at grompp time. Could anyone explain the difference? trevor pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top editconf -f fws.g

[gmx-users] Water models usage info

2011-01-09 Thread trevor brown
included in the list, look at the "pdb2gmx" title at the end of the manual. trevor On 10/01/2011 2:41 AM, trevor brown wrote: > Dear friends, > My run commands are below. It works without any error. > However if I add -water tip3p at the end of pdg2gmx ... line it causes >

[gmx-users] topoloy for CNT

2011-01-12 Thread trevor brown
Dear friends, My aim is to establish a topology for a CNT. My commands and the error are below. Does anyone tell me what I should do? trevor COMMANDS: editconf -f cnt.pdb -o box.gro -c -box 8.0 8.0 8.0 genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro g_x2top -f box.gro -o box.top -p

[gmx-users] CNT

2011-01-15 Thread trevor brown
Dear users, In Gromacs 4.5.3, atom types are defined in /share/top/oplsaa.ff/atomtypes.atp. The corresponding bonds for diffrent atopm pairs are described as between opls_001 and opls_965. I have a CNT, I need C-C intereaction, which one should I choose? Second question; where can I find info about

[gmx-users] CNT

2011-01-17 Thread trevor brown
Dear friends, I have constructed a .top file for a CNT by g_x2top. to do this I have added C-C interactions in .n2t file and also related ff in .atomtypes.atp. I have also a .top file for a peptide by pdb2gmx. My aim is to construct a simulation system in which I want to see the adsorption. I don'

[gmx-users] Re:Re: CNT

2011-01-18 Thread trevor brown
wishes trevor On 18/01/2011 10:25 AM, trevor brown wrote: > Dear friends, > I have constructed a .top file for a CNT by g_x2top. to do this I > have added C-C interactions in .n2t file and also related ff in > .atomtypes.atp. I have also a .top file for a peptide by pdb2gmx. > My aim

[gmx-users] CNT

2011-01-18 Thread trevor brown
Dear friends, I have the following topology for system including CNT+peptide+water When I grompp for minimization, I got the following error. How can I solve it? best wishes trevor WARNING 1 [file ffbonded.itp, line 2703]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C

[gmx-users] grompp error

2011-01-18 Thread trevor brown
Dear users, I have the following error with grompp before minimization. I defined opls_996 for C atom by myself. Any suggetions to solve it? best trevor WARNING 1 [file ffbonded.itp, line 2703]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210478900 ERR

[gmx-users] CNT

2011-01-19 Thread trevor brown
Dear Justin, Regarding our previous discussion under "CNT" topic, you want to know exactly what I did to define C-C interaction. I have summarized it below. 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t Copls_9950 12.011 2C

[gmx-users] CNT

2011-01-19 Thread trevor brown
Hi Justin, I added lines to ffnonbonded.itp. It resulted in following error. It has some warnings and an error. I am interested in error. After that I will look at the warnings. In which file we may have an error? It is not specified. best wishes trevor Generated 335790 of the 335790 non-bonded

[gmx-users] (no subject)

2011-01-20 Thread trevor brown
Dear users, How can we fix the position of some atoms? best wishes trevor -- 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)

[gmx-users] (no subject)

2011-01-25 Thread trevor brown
Dear Justin/Mark, I would like to have a private course about Gromacs in Holland. Is there such a facility for this? Who should I talk with? Or is there a workshop in near future? best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] gro to itp

2011-01-27 Thread trevor brown
Dear all, I obtained a gro file with g_x2top for a CNT. I deleted [commands] in t and saved it as XXX.itp Is it true? If no, how can I convert it into .itp? best, trevor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv