[gmx-users] error with grompp

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

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.

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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>>
>
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