Hi Justin,<br><br>Thanks a lot!<br>Things worked.<br><br>Now I, however, have a different problem in extension to what I am doing.<br><br>I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion.<br>
<br> editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro<br> genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro<br> genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro<br> editconf -f his20.gro -d 0 -o onlyhis.gro<br>
editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro<br> genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro<br><br><br>Now I need to add few more Li ions and anions in the sphere.<br><br>I tried doing that,<br>genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top <br>
<br>(1dhb.gro is 2,5-dihydrobenzoic acid anion)<br><br>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.<br>
<br>How can I place all the anions and then Li+ ions specifically inside the sphere?<br><br>Thanks a lot,<br>SN<br><br><div class="gmail_quote">On Wed, May 25, 2011 at 1:18 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
<br>
shivangi nangia wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Justin,<br>
<br>
<br><div><div></div><div class="h5">
Revisiting some of the calculations I had tried to do few days back.<br>
<br>
Just as a recap I am trying to build a sphere around the protein.<br>
<br>
As you had suggested in the last messgae of this thread to make a new directory. I did that.<br>
<br>
I used the following commands:<br>
<br>
editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro<br>
genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro<br>
genbox -cp his1.gro -cs li_sol.gro<br>
<br>
*<br>
1li.gro is:*<br>
1 Li ion<br>
1<br>
1LI+ LI 1 1.736 0.839 0.257<br>
1.86824 1.86824 1.86824<br>
<br>
*onlyli.gro is:*<br>
1 Li ion<br>
1<br>
1LI+ LI 1 7.500 7.500 7.500<br>
15.00000 15.00000 15.00000<br>
<br>
*mix.gro ( pre-made mix of 1:1 :: water: methanol)*<br>
<br>
li_sol.gro des look like a sphere after seeingin vmd.<br>
<br>
his1.gro is:<br>
UNNAMED<br>
14<br>
1HISH N 1 0.000 0.000 0.000<br>
1HISH H1 2 -0.033 0.000 -0.094<br>
1HISH H2 3 -0.033 -0.082 0.047<br>
1HISH CA 4 0.146 0.000 0.000<br>
1HISH CB 5 0.204 0.120 -0.077<br>
1HISH CG 6 0.291 0.076 -0.190<br>
1HISH ND1 7 0.240 0.009 -0.299<br>
1HISH HD1 8 0.145 -0.014 -0.315<br>
1HISH CD2 9 0.425 0.089 -0.215<br>
1HISH CE1 10 0.345 -0.019 -0.382<br>
1HISH NE2 11 0.458 0.027 -0.333<br>
1HISH HE2 12 0.549 0.020 -0.374<br>
1HISH C 13 0.195 0.000 0.146<br>
1HISH O 14 0.118 0.000 0.242<br>
2.50220 0.24060 2.47531<br>
<br>
<br>
<br>
I get the following error yet again:<br>
<br>
Fatal error:<br>
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.<br>
<br>
<br>
</div></div></blockquote>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
------------------------------------------------------<br>
<br>
Thanks a lot in advance.<br>
<br>
Sorry about reviving few days old thread.<br>
<br>
<br>
Thanks,<br>
SN<br>
<br>
<br>
<br>
<br></div><div class="im">
On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
shivangi nangia wrote:<br>
<br>
Hi Justin,<br>
<br>
I used 15 nm cubic box and 6 nm shell.<br>
I again tried to insert only 1 histidine molecule in the sphere.<br>
I get the same error<br>
<br>
Fatal error:<br>
One of the box vectors has become shorter than twice the cut-off<br>
length or box_yy-|box_zy| or box_zz has become smaller than the<br>
cut-off.<br>
<br>
<br>
<br>
Please provide the exact command that gives the error. I cannot<br>
reproduce this using a shell value less than half a box vector. You<br>
may also want to try starting from a clean directory - get rid of<br>
old files and intermediates so you're sure you're using the right files.<br>
<br>
-Justin<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<tel:%28540%29%20231-9080><div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>