jorge_quint...@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_quint...@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_quint...@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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
