[gmx-users] Solvation Free energy using Amber

[jorge_quintero at ciencias.uis.edu.co]

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.

[ 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>