[gmx-users] error with grompp

[Justin A. Lemkul]

On 6/29/12 5:38 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
>
> yes I removed all the old resulting files and did everything again. So now
> there is the topology and coordinate file with only NA and CL and not NA+
> or CL-.
> I also checked whether the molecules are listed in the same order as in
> the .gro file and it is the case. So that is also correct.
>
> What do you mean with:
>
>> What does your [molecules] directive specify?
>
> My [molecules] part in the topology file looks like this:
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DUM             20088
> SOL         13428
> NA               29
> CL               29
>

I see no reason this would not work.  However, I just noticed from your previous 
message:

>>> ; Include water topology
>>> #include "amber03.ff/tip3p.itp"
>>>
>>>
>>>
>>> ; Include topology for ions
>>> #include "amber03.ff/ions.itp"
>>>
>>> #include "amber03.ff/spc.itp"
>>> #include "amber03.ff/dum.itp"
>>>

You're using two different water models, so things are getting overridden there. 
  With AMBER03, you should be using TIP3P, not SPC.  The conflicting water 
models suggest you've made manual modifications to the topology.  Perhaps there 
is some error as a result.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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