[gmx-users] Solvation Free energy using Amber

[Justin A. Lemkul]

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

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