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