Hi Yang,<br>
I was thinking to set mass_B to 0 but what I
was supposed to do is converting dummy atoms to H atoms. In my opinion,
it wouldn't be H atoms if I set the mass to 0. Am I thinking wrong?<br>
Thank you.<br>
<br>
Regards,<br>
Qin<br><br><div><span class="gmail_quote">On 9/11/07, <b class="gmail_sendername">Yang Ye</b> <<a href="mailto:leafyoung@yahoo.com">leafyoung@yahoo.com</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;">
you have set the mass_B to 0 as well.<br><br>On 9/11/2007 10:54 PM, 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<br>> force 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>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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