Karel Berka wrote:
Hi all,
I have detected that preference in reading forcefield files in Gromacs
4.5 has probably been changed from Gromacs 4.0.x and older.
In older gromacs, when there was forcefield with modification present in
my working directory, then it was read preferentially, but now it seems
that forcefield is primarily read from /share/top directory - Am I right?
The working directory is still searched first.
In 4.5.2 I have tried to have modified gromos53a6.ff in my working
directory, but the modification was not used by gromacs.
What do you mean "not used"? Was the wrong force field called when using
pdb2gmx? Gromacs prints a list of force field subdirectories in the working
directory, then in GMXLIB, and allows you to choose. In the 4.5.x series, you
need a full working subdirectory of the modified force field.
The only way around was to rename the files in any of these manners:
1) directory to gromos53a6b.ff and
forcefield.itp therein to have include gromos53a6b.ff/ffnonbonded.itp
and gromos53a6b.ff/ffbonded.itp
and point md.top to gromos53a6b.ff/forcefield.itp
This should not be necessary.
or
2) simply copy all files from ff directory to root and mention them in
md.top (forcefield.itp has to be changed afterwards)
Copying all the files from the desired *.ff subdirectory into the working
directory (of whatever name you choose) is a correct procedure. There should be
no need to manually modify the .top file, unless you're somehow manually
generating it, as well. With pdb2gmx, the modified files can be read like any
other force field.
-Justin
However both of these modifications are rather messy.
--
Zdraví skoro zdravý
Karel "Krápník" Berka
****************************************************************
RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769
fax: +420-585634769
e-mail: karel.be...@upol.cz <mailto:karel.be...@upol.cz>
****************************************************************
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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