Hi Justin, Thanks a lot! Things worked.
Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro editconf -f his20.gro -d 0 -o onlyhis.gro editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro Now I need to add few more Li ions and anions in the sphere. I tried doing that, genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top (1dhb.gro is 2,5-dihydrobenzoic acid anion) But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? Thanks a lot, SN On Wed, May 25, 2011 at 1:18 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shivangi nangia wrote: > >> Hi Justin, >> >> >> Revisiting some of the calculations I had tried to do few days back. >> >> Just as a recap I am trying to build a sphere around the protein. >> >> As you had suggested in the last messgae of this thread to make a new >> directory. I did that. >> >> I used the following commands: >> >> editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro >> genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro >> genbox -cp his1.gro -cs li_sol.gro >> >> * >> 1li.gro is:* >> 1 Li ion >> 1 >> 1LI+ LI 1 1.736 0.839 0.257 >> 1.86824 1.86824 1.86824 >> >> *onlyli.gro is:* >> 1 Li ion >> 1 >> 1LI+ LI 1 7.500 7.500 7.500 >> 15.00000 15.00000 15.00000 >> >> *mix.gro ( pre-made mix of 1:1 :: water: methanol)* >> >> li_sol.gro des look like a sphere after seeingin vmd. >> >> his1.gro is: >> UNNAMED >> 14 >> 1HISH N 1 0.000 0.000 0.000 >> 1HISH H1 2 -0.033 0.000 -0.094 >> 1HISH H2 3 -0.033 -0.082 0.047 >> 1HISH CA 4 0.146 0.000 0.000 >> 1HISH CB 5 0.204 0.120 -0.077 >> 1HISH CG 6 0.291 0.076 -0.190 >> 1HISH ND1 7 0.240 0.009 -0.299 >> 1HISH HD1 8 0.145 -0.014 -0.315 >> 1HISH CD2 9 0.425 0.089 -0.215 >> 1HISH CE1 10 0.345 -0.019 -0.382 >> 1HISH NE2 11 0.458 0.027 -0.333 >> 1HISH HE2 12 0.549 0.020 -0.374 >> 1HISH C 13 0.195 0.000 0.146 >> 1HISH O 14 0.118 0.000 0.242 >> 2.50220 0.24060 2.47531 >> >> >> >> I get the following error yet again: >> >> Fatal error: >> One of the box vectors has become shorter than twice the cut-off length or >> box_yy-|box_zy| or box_zz has become smaller than the cut-off. >> >> >> > Look at the box vectors of his1.gro - a sphere of solvent with a radius of > 6 cannot fit inside a box that is 2.5 x 0.2 x 2.5 nm^3. > > -Justin > > ------------------------------------------------------ >> >> Thanks a lot in advance. >> >> Sorry about reviving few days old thread. >> >> >> Thanks, >> SN >> >> >> >> >> On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> shivangi nangia wrote: >> >> Hi Justin, >> >> I used 15 nm cubic box and 6 nm shell. >> I again tried to insert only 1 histidine molecule in the sphere. >> I get the same error >> >> Fatal error: >> One of the box vectors has become shorter than twice the cut-off >> length or box_yy-|box_zy| or box_zz has become smaller than the >> cut-off. >> >> >> >> Please provide the exact command that gives the error. I cannot >> reproduce this using a shell value less than half a box vector. You >> may also want to try starting from a clean directory - get rid of >> old files and intermediates so you're sure you're using the right >> files. >> >> -Justin >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 list gmx-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 >
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