<div>Looks fine to me.</div>
<div>you can add 18 positive (Na) ions to neutralise.<br><br> </div>
<div><span class="gmail_quote">On 10/19/06, <b class="gmail_sendername">"Stefan Schöbel"</b> <<a href="mailto:s.schoebel1@gmx.net">s.schoebel1@gmx.net</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I am using only a protein and the GROMOS96 43a1 force field.<br>After pdb2gmx I got:<br>Back Off! I just backed up
test.top to ./#test.top.3#<br>Processing chain 1 (1594 atoms, 214 residues)<br>There are 288 donors and 315 acceptors<br>There are 479 hydrogen bonds<br>Will use HISB for residue 45<br>Will use HISB for residue 79<br>Will use HISB for residue 177
<br>Will use HISB for residue 202<br>Checking for duplicate atoms....<br>Now there are 1593 atoms. Deleted 1 duplicates.<br>Opening library file /home/mpaetzel/programs/share/gromacs/top/specbond.dat<br>5 out of 5 lines of
specbond.dat converted succesfully<br>Special Atom Distance matrix:<br> CYS102<br> SG760<br>CYS167 SG1251 2.930<br>N-terminus: NH3+<br>C-terminus: COO-<br>Now there are 214 residues with 1957 atoms
<br>Making bonds...<br>Opening library file /home/mpaetzel/programs/share/gromacs/top/aminoacids.dat<br>Number of bonds was 1996, now 1991<br>Generating angles, dihedrals and pairs...<br>Before cleaning: 3360 pairs<br>Before cleaning: 3782 dihedrals
<br>There are 1101 dihedrals, 946 impropers, 2896 angles<br> 3360 pairs, 1991 bonds and 0 virtual sites<br>Total mass 22620.601 a.m.u.<br>Total charge -18.000 e<br>Writing topology<br><br><br>--> why are the HIS residues changed into HISB?
<br><br>after editconf:<br><br>Generated 279 of the 1225 non-bonded parameter combinations<br>Excluding 3 bonded neighbours for Protein 1<br>Excluding 2 bonded neighbours for SOL 7683<br>Excluding 2 bonded neighbours for SOL 2730
<br>NOTE:<br>System has non-zero total charge: -1.800000e+01<br><br><br>I tried adding C term Oxygen with spdbv as well, but it still the same uneven charge.<br><br>What happened?<br><br>thanks in advance<br><br>Stefan<br>
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Research Assistant,<br>Old Dominion University,<br>Norfolk, Va-23529.