Thank you so much. <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;">
On 9/12/2007 12:39 AM, Wang Qin wrote:<br>> Hi Yang,<br>> I was thinking to set mass_B to 0 but what I was supposed to do<br>> is converting dummy atoms to H atoms. In my opinion, it wouldn't be H<br>> atoms if I set the mass to 0. Am I thinking wrong?
<br>it's an H as long as it shares the same VDW as H and it carries the same<br>charge as H.<br>> Thank you.<br>><br>> Regards,<br>> Qin<br>><br>> On 9/11/07, *Yang Ye* <<a href="mailto:leafyoung@yahoo.com">
leafyoung@yahoo.com</a><br>> <mailto:<a href="mailto:leafyoung@yahoo.com">leafyoung@yahoo.com</a>>> wrote:<br>><br>> 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<br>> 0.000000<br>> ><br>> > I changed the both of the mass_A to 0.00000, but that<br>> didn't help.<br>> > Does anyone have ideas on that?
<br>> > Thank you very much.<br>> ><br>> > Regards,<br>> > Qin<br>> ><br>> ------------------------------------------------------------------------<br>> >
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