<div>Hi Maik,</div>
<div> I really did mix up a dummy atom with a virtual site. Any difference?</div>
<div> Thank you very much for your help.</div>
<div> </div>
<div>Regards,</div>
<div>Qin<br><br> </div>
<div><span class="gmail_quote">On 9/12/07, <b class="gmail_sendername">Maik Goette</b> <<a href="mailto:mgoette@mpi-bpc.mpg.de">mgoette@mpi-bpc.mpg.de</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">The problem actually is, that you mixed up a dummy atom with a virtual<br>site, I guess.<br><br>Virtual sites are not allowed to have a mass, as the error message
<br>claims. Also, a proper hydrogen should have a mass.<br><br>If you want a hydrogen to appear, you have to place a particle in<br>A-state which has no non-bonded interaction, i.e. LJ & QQ interactions<br>should be zero. If you want to prevent it from flying away, you should
<br>put bonded terms to the particle.<br>In the B-state, the QQ and LJ should be there (whereas the LJ<br>interaction for a hydrogen is 0 anyway).<br><br>21 opls_999 1 LG4 H21 21 0.0000 1.00800
<br> opls_172 0.4650 1.00800<br><br>opls_999 DUM 0 1.008000 0.000 A 0.000000 0.000000<br><br>So, I expect, this is, how it should look like.<br>Be aware of the missing bonded terms in the force field for a DUM
<br>particle. Maybe, you want to call it H instead...<br><br>Regards<br><br>Maik Goette, Dipl. Biol.<br>Max Planck Institute for Biophysical Chemistry<br>Theoretical & computational biophysics department<br>Am Fassberg 11
<br>37077 Goettingen<br>Germany<br>Tel. : ++49 551 201 2310<br>Fax : ++49 551 201 2302<br>Email : mgoette[at]mpi-<a href="http://bpc.mpg.de">bpc.mpg.de</a><br> mgoette2[at]gwdg.de<br>WWW : <a href="http://www.mpibpc.gwdg.de/groups/grubmueller/">
http://www.mpibpc.gwdg.de/groups/grubmueller/</a><br><br><br>Wang Qin wrote:<br>> Hi there,<br>> I met the problem when I ran "grompp", the errors are:<br>> ERROR 1 [file "po4lig4tip3.top", line 26741]:
<br>> virtual site H21 (Res LG4-173) has non-zero mass 1.008<br>> Check your topology.<br>><br>> ERROR 2 [file "po4lig4tip3.top", line 26741]:<br>> virtual site H22 (Res LG4-173) has non-zero mass
1.008<br>> Check your topology.<br>><br>> Then I checked my topology file, here were the definition of<br>> LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms)<br>> ;nr type resnr residue atom cgnr charge
<br>> mass type_B charge_B mass_B<br>> 21 opls_999 1 LG4 H21 21 0.0000<br>> 1.00800 opls_172 0.4650 1.00800<br>> 22 opls_999 1 LG4 H22 22
0.0000<br>> 1.00800 opls_172 0.4650 1.00800<br>><br>> in which opls_999 was from what I defined by myself in the force<br>> field itp file:<br>> opls_999 DUM 0 1.008000 0.000
V 0.000000 0.000000<br>><br>> I changed the both of the mass_A to 0.00000, but that didn't help.<br>> Does anyone have ideas on that?<br>> Thank you very much.<br>><br>> Regards,
<br>> Qin<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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