----- 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 <[email protected]>
> > ----- Original Message ----- > > From: Jens Pohl <[EMAIL PROTECTED]> > > Date: Thursday, February 14, 2008 12:25 am > > Subject: [gmx-users] Strange output with Genbox > > To: [email protected] > > > > > 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 _______________________________________________ gmx-users mailing list [email protected] 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
