[gmx-users] Membrane tutorial regarding,

[RAHUL SURESH]

Dear Justin,

Why there are 6 equilibrations MDP's generated and how could I use one?
Which one should be opted for?


I found a Readme python script and is that one should be executed it?

Thank you

On Tue, Apr 10, 2018 at 11:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/10/18 2:21 PM, RAHUL SURESH wrote:
>
>> Dear Users,
>>
>> Performing membrane simulations using charmm36 ff. The Protein/membrane
>> system is constructed using charmm-gui [POPC] . The system was then used
>> in
>> gromacs 2016.4 for simulation . Following the simulation tutorial,
>>
>> *gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter
>> -water spc*
>>
>
> You shouldn't be doing this. CHARMM should not be used with SPC, and in
> fact if you built the system with CHARMM-GUI you have all the topologies
> and input files necessary to proceed directly with energy minimization,
> equilibration, etc.
>
> -Justin
>
> NH2 and COOH were chosen as terminals.
>>
>> But bad luck its shows a fatal error.
>>
>> *fatal error:*
>> *There were 49308 missing atoms in molecule Protein if you want to use
>> this*
>> *incomplete topology anyhow, use the option -missing*
>>
>> All the missing atoms were only hydrogen.
>>
>> the water model was then changed to tip3p, even the error prevails.
>>
>> Why the ignh flag doesn't work here?
>> Can I go with -missing?
>>
>> Thank you
>>
>>
> --
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*