<p>Hi Mohsen,</p>
<p>I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Jan 6, 2011 7:22 PM, "mohsen ramezanpour" <<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>> wrote:<br><br>Dear Amit<br>I entered these commands for rotating box:<br>
editconf -f conf.gro -o output.pdb -rotate 0 0 25.4<br>and then:<br>editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 <br>as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet.<br>
thanks in advance for your attention and reply<p><font color="#500050">
On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey <<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>> wrote:
>
> Could you post the e...</font></p><br>--<br>
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