[gmx-users] Solvation Free energy using Amber

[Justin A. Lemkul]

jorge_quintero at ciencias.uis.edu.co wrote:
> Well,
> 
> The main reason why I've testedd to obtain solvation free energy (SFE) for
> toluene is because I want to do it for my future studies related with
> dimer SFE employing Amber force field with gromacs 4.0. Recently, I've
> read the tutorial. But, when I tried to do the same, I got some errors
> during tpr file constructing.  So I really don't know how to do it.
> 

If you post what the errors are, you stand a much better chance of getting 
useful advice.  There are other resources posted on the Gromacs site that are 
excellent references that you can refer to, as well.

-Justin

> 
> best regards
> 
> 
>>
>> jorge_quintero at ciencias.uis.edu.co wrote:
>>> Dear Justin
>>>
>>> I removed the semicolons but my calculations don't work.  The problem is
>>> how can I add the other parameters -like bonds, angles and dihedrals-
>>> for
>>> B-state.  I've tried to add it, but I get some problems to obtain the
>>> tpr
>>> file.  Thanks again.
>>>
>> Please read the manual, section 5.7.4.  I don't see why you need to mutate
>> bonded interactions for a solvation free energy calculation.  For toluene,
>> there
>> is even a tutorial available at the following link.  It is for a different
>> force
>> field, but should still be useful:
>>
>> http://md.chem.rug.nl/education/Free-Energy_Course/index.html
>>
>> Also, from your original topology, you should not turn off charges and L-J
>> interactions simultaneously; doing so will lead to very large errors.
>> These
>> transformations should be done separately.  Please refer to the wiki page
>> on the
>> Gromacs site and the numerous discussions in the list archive about proper
>> procedure.  The tutorial above will also help.
>>
>> -Justin
>>
>>> [ bonds ]
>>>     1     2     1  --> how can I write the B-state parameters??
>>> .............
>>> [ angles ]
>>>     2     1     3     1  ???
>>> .............
>>> [ dihedrals ]
>>>     2     1     4     5     3   ?????
>>>
>>>
>>> Best regards
>>>
>>>> jorge_quintero at ciencias.uis.edu.co wrote:
>>>>> Dear all.
>>>>>
>>>>> I've tried to calculate solvatin free energy using amber force field
>>>>> and
>>>>> gromacs but unfourtunately I can't include the parameters for B type.
>>>>> Can
>>>>> somebody help me with that, I send you a top file.
>>>>>
>>>> All of your B-state parameters are commented out.  Remove the
>>>> semicolons.
>>>>
>>>> -Justin
>>>>
>>>>> Best regards,
>>>>>
>>>>>
>>>>> Jorge R. Quintero
>>>>> Grupo de Investigación en Fisicoquímica Teórica y Experimental
>>>>> (GIFTEX)
>>>>> Universidad Industrial de Santander
>>>>> Escuela de Química
>>>>> Bucaramanga, Santander - Colombia
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> 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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>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> 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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> 
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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