[gmx-users] Membrane tutorial regarding,

[Justin Lemkul]

On 4/10/18 2:58 PM, RAHUL SURESH wrote:
> Dear Justin,
>
> Why there are 6 equilibrations MDP's generated and how could I use one?
> Which one should be opted for?

All of them, in sequence, if you want to follow the recommended Membrane 
Builder protocol (you should read that reference if you haven't already 
so you know what the Membrane Builder is doing and what the 
equilibration scheme actually does).

-Justin

>
> 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
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================