[gmx-users] error with grompp

[Mark Abraham]

On 07/02/2012 06:12 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Okey thank you.
> But shell I also
>
> #include "amber03.ff/spc.itp"
>
> Because when I don't include it I get the error:
>
> Fatal error:
> No such moleculetype SOL
>
> An when I include it there is no error.

The only thing that makes sense is to use only amber03/tip3p.itp, like 
Justin said. It defines the SOL [moleculetype], so your observations do 
not seem consistent with #including such a file. Your .top fragment 
suggests you're #including them at quite different points, and maybe the 
point at with you #include tip3p is inappropriate (e.g. inside an #ifdef).

Mark

> But in one of the last mails Justin wrote that:
>
> "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."
>
>
>
>> On 07/02/2012 05:49 PM, reisingere at rostlab.informatik.tu-muenchen.de
>> wrote:
>>> Hi Justin,
>>> I wanted to use the only tip3p but I do not have the tip3p.gro file but
>>> only the tip3p.tip file.
>> http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file
>>
>>>    I also have the tip4p.gro and tip5p.gro file. Can
>>> I also use them?
>> No.
>>
>> Mark
>>
>>>> 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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>