[gmx-users] Solvation Free energy using Amber

[jorge_quintero at ciencias.uis.edu.co]

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.


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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