[gmx-users] error with grompp

[Mark Abraham]

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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>