[gmx-users] error with grompp

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Justin,
I wanted to use the only tip3p but I do not have the tip3p.gro file but
only the tip3p.tip file. I also have the tip4p.gro and tip5p.gro file. Can
I also use them?

>
>
> 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
>
> --
> ========================================
>
> 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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