Dear Gromacs users<br><br>I have a very strange problem when using pdb2gmx in the gromacs 4.5.3. I looked up the mailing list but I can't find something similar.<br><br>I have in a .pdb file a crystalline substrate consisting of Si particles. <br>
<br>By running in previous gromacs version (i.e. gromacs 3.3) :<br><br><i>pdb2gmx -f name.pdb -p topol.top -o output.gro<br></i><br>I get the following result for the <i><b>topol.top</b> </i>file<b>:</b><br><br>[ atoms ]<br>
; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 SI 1 ZZZ D1 1 0 28.08 ; qtot 0<br> 2 SI 1 ZZZ D2 2 0 28.08 ; qtot 0<br>
3 SI 1 ZZZ D3 3 0 28.08 ; qtot 0<br> 4 SI 1 ZZZ D4 4 0 28.08 ; qtot 0<br> 5 SI 1 ZZZ D5 5 0 28.08 ; qtot 0<br>
etc<br><br>which of course is normal, but by doing the same in gromacs 4.5.3, the <b><i>topol.top </i></b>file<b><i> </i></b>is the following:<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
; residue 1 ZZZ rtp ZZZ q 0.0<br> 1 SI 1 ZZZ D1 1 0 28.08 ; qtot 0<br> 2 O 1 ZZZ D2 2 0 1.48594e-41 ; qtot 0<br> 3 O 1 ZZZ D3 3 0 1.48594e-41 ; qtot 0<br>
4 O 1 ZZZ D4 4 0 1.48594e-41 ; qtot 0<br> 5 O 1 ZZZ D5 5 0 1.48594e-41 ; qtot 0<br>etc<br><br>I have no idea where these O come from.<br><br>
Did anyone have similar problems?<br><br>Best regards, Chrysostomos<br><br><br><br>