> ----- Original Message ----- > From: Jens Pohl <[EMAIL PROTECTED]> > Date: Thursday, February 14, 2008 5:56 pm > Subject: Re: [gmx-users] Strange output with Genbox > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > > ----- Original Message ----- > > > From: Jens Pohl <[EMAIL PROTECTED]> > > > Date: Thursday, February 14, 2008 12:25 am > > > Subject: [gmx-users] Strange output with Genbox > > > To: gmx-users@gromacs.org > > > > > > > Hello! > > > > > > > > I try to simulate a modified protein in a water-box. When I > > use > > > > genbox and have a look on the output-file then the water > > > > molecules are located in between the AA-sequence which > > results > > > > in an "exploding" molecule during the mdrun. I've done it > > > > several times from the very beginning, always getting a > > similar > > > > result (distribution of water in the AA sequence varied a > > bit). > > > > > > > > Input-sequence (AA): > > > > MGVLAI... > > > > > > > > Output after genbox: > > > > OMOGOOVOLOAOIOO... > > > > > > It's not easy to be sure exactly what you're describing here, > > but I think you mean that genbox is placing waters inside the > > expected vdW surface of your protein. If so, then check out > > "genbox -h" for how GROMACS works out this surface. Otherwise, > > please consider posting a picture to a website somewhere. > > > > The water is placed in between the chain. When I have a look at > > the sequence there is water followed by AA followed by water. > > I've done a similar simulation before and there the sequence was > > Protein first and the the water residues. > > Genbox doesn't change your solute topology, so it is certainly not changing > your sequence. > > Mark
The topology seems to be ok. The only difference between editconf and genbox is the number of solutes. So it might be just a problem with the depiction of the system combined with unsufficient EM? I'll try it, hope the best and report the results. Thank you very much Jens _______________________________________________________________________ Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
