<div>Hi!</div>
<div>you usually get that type of output when the order in which the molecule atoms are written in the topology file (in the itp in your case) does not correspond to the order in the gro file; it might just be that you call the itp corresponding to the second molecule written in the gro file before calling the itp corresponding to the first one. grompp absolutely needs the same order for the atoms to match them correctly.
</div>
<div>hope it helps,</div>
<div> </div>
<div>regards,</div>
<div>Giovanna<br><br> </div>
<div><span class="gmail_quote">On 8/21/06, <b class="gmail_sendername">Marc Charendoff</b> <<a href="mailto:mcharend@sbcglobal.net">mcharend@sbcglobal.net</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hello,<br><br>I'm running grompp on two small molecules in a single<br>.gro file using the following topology file:
<br><br>#include "ffgmx.itp"<br>#include "BDEX.ITP"<br>#include "AHL.ITP"<br>#include "spc.itp"<br><br>[ system ]<br>BDEX<br>AHL<br><br>[ molecules ]<br>BDEX 1<br>AHL 1<br>
<br>Part of my output looks like the following:<br><br>Back Off! I just backed up mdout.mdp to<br>./#mdout.mdp.2#<br>checking input for internal consistency...<br>calling cpp...<br>processing topology...<br>Generated 1284 of the 1485 non-bonded parameter
<br>combinations<br>Excluding 3 bonded neighbours for BDEX 1<br>Excluding 3 bonded neighbours for AHL 1<br>processing coordinates...<br>WARNING 1 [file "topol.top", line 12]:<br>Bad box in file Complex.GRO<br>
Generated a cubic box 20.000 x 1.445 x 1.830<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (O2 - CAS)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (HAA - CAR)<br>Warning: atom names in
topol.top and Complex.GRO don't<br>match (C2 - CAQ)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (C3 - CAP)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (O3 - CAO)<br>Warning: atom names in
topol.top and Complex.GRO don't<br>match (HAB - CAN)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (C4 - CAM)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (O4 - CAL)<br>Warning: atom names in
topol.top and Complex.GRO don't<br>match (C5 - CAK)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (C6 - CAJ)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (O6 - OAT)<br>Warning: atom names in
topol.top and Complex.GRO don't<br>match (HAC - CAI)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (O5 - CAH)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (C1 - OAU)<br>Warning: atom names in
topol.top and Complex.GRO don't<br>match (O1 - N)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (CAJ - HAA)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (CAK - CA)<br>Warning: atom names in
topol.top and Complex.GRO don't<br>match (OBY - CB)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (CAL - CAA)<br>Warning: atom names in topol.top and Complex.GRO don't<br>match (OBZ - OAC)<br>(more than 20 non-matching atom names)
<br>WARNING 2 [file "topol.top", line 12]:<br>120 non-matching atom names<br>atom names from topol.top will be used<br>atom names from Complex.GRO will be ignored<br><br>- Complex.GRO consists of two molecules AHL and BDEX.
<br>-The ffgmx force field has already worked successfully<br>with the BDEX.itp and molecule, but for some reason<br>all but 2 of the AHL molecule atoms have the mismatch<br>problem. Which file do I have to modify to clear the
<br>atom name mismatch issue? The atom names in question<br>are identical between the Complex.gro and AHL.itp<br>files, so I'm a bit confused. Any guidance you could<br>provide would be appreciated.<br><br>Regards,<br>Marc
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