Hi ALpay,<br>
<br>
For computational reasons, gromacs usually uses the rectangular box
corresponding to the (probably more complex) shape you are using. This
is no problem, since it is always possible to convert a system in one
box type into any other box type, available under pbc. The
configuration of the infinite simulation system is not changed.<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 2/12/06, <b class="gmail_sendername">Nuri A Temiz</b> <<a href="mailto:temiz+@pitt.edu">temiz+@pitt.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello gmx users<br>><br>>I am trying to simulate a Zinc-finger domain. I have searched the mailing<br>list<br>>about Zn-ligand interactions and i decided to fix the Zn since i am only<br>>interested in keeping the fold stable.
<br>>But when i use pdb2gmx, the program automatically protonates the Cys S and<br>His<br>>NE2. I have checked the manual and fixed the His protonation states, but<br>>could not change the Cys residues. In the manual, the section for Pdb2gmx
<br>>says that the program can be prompted to change Cys residueprotonation state,<br>>but i did not see the option to do it.<br><br>>I must also add that i just started to use Gromacs, so i may be missing<br>>something.
<br> I have sent this email yesterday. I have already tried -cys on pdb2gmx which<br>actually is not an option. Then i changed my cysteines by hand on topology<br>file and added constraints on 2 cysteines,2 histidines and Zn, also
<br>renumbered the topology and gro files.<br><br>But everytime i use editconf and genbox, most of my solvent is out od the<br>box. I checked the box visually, the solute (zn-finger peptide) is in the<br>center but about 3/4 of the solvent is out of the box.
<br><br>here are the commands i used for editconf and genbox''<br><br><br>editconf -f speptide -o -bt dodecahedron -d 1.5<br>genbox -cp out -cs -p speptide -o b4em<br><br>by the way, i use gromacs 3.2.1<br>any help would be great
<br><br>in the md it should not be a problem since i use pbc.<br><br>but why do i see the shift in the solvent molecules visually when i use either<br>vmd or ngmx.<br><br>Thank you very much.<br>ALpay<br>--<br>N. Alpay Temiz
<br>Department of Computational Biology &<br>Department of Molecular Genetics and Biochemistry<br>School of Medicine, University of Pittsburgh<br><a href="mailto:e-mail:temiz@pitt.edu">e-mail:temiz@pitt.edu</a><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>
Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>