On 18/05/2012 8:02 PM, francesco oteri wrote:
Hi,
at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can
find the files I am using
Files ffcharmmnb.itp ffcharmmbon.itp have been generated through:
convert_charmm_to_gromacs.pl
<http://convert_charmm_to_gromacs.pl/> par_all36_carb.prm
while carbohydrates.rtp and carbohydrates.rtp through a script of mine.
Now, if you look at [ dihedraltypes ] section in file ffcharmmbon.itp,
there are strange things:
1) dihedrals defined once, are converted Ryckaert-Bellemans form,
while the armonic form should be more clear.
Anyway, it just a matter of style so I dont complan about.
2) dihedrals with multiple definitions ( OC30P CC3162 CC3161 OC311 at
line 598 in file ffcharmmbon.itp, for example) are defined as:
OC30P CC3162 CC3161 OC311 3 20.92 41.84 16.74 -41.84 0 0
; 30P CC3162 CC3161 OC311 1 180 10.46 1
; 30P CC3162 CC3161 OC311 1 0 8.368 2
; 30P CC3162 CC3161 OC311 1 0 10.46 3
The commented lines clearly display the multiple definition, that can
be described using function 9
... which didn't exist at the time of my writing of that script, as the
comments in the script discuss. Hence solution 1), which was adequate
for the subset of CHARMM27 that was of interest to me.
3) An other problem rise with impropers dihedrals. Any of them are
defined as Ryckaert-Bellemans,
ex. HCA1 CC3161 CC3162 OC311 3 0.5858 1.757 0 -2.343 0 0
at line 926 of ffcharmmbon.itp
while points 1 and 2 don't impact on the correctness of the
simulation and can be bypassed defining
[ bondedtypes ] section as following
1 5 3 2 1 3 1 0
Problem 3 cannot be solved without manipulating the ffcharmmbon.itp.
In fact, since some impropers are defined as functiontype 2 other as
functiontype 3,
so there is not an unique bondedtypes definition covering both the
definition.
Did I any mistake or actually there is a problem in the script?
IIRC CHARMM36 is more recent than that script, so the assumptions made
by the script for CHARMM27 may not be applicable. If CHARMM36 uses more
than one kind of improper dihedral, then I would not expect the script
to function correctly in this regard. You would need to modify the
script or its output.
Mark
Francesco
2012/5/18 Mark Abraham <[email protected]
<mailto:[email protected]>>
On 18/05/2012 2:52 AM, francesco oteri wrote:
Dear gromacs users,
I am trying to port a set of charm parameter in gromacs.
I am using the script convert_charmm_to_gromacs.pl
<http://convert_charmm_to_gromacs.pl> contained in the
file charmm_to_gromacs.tgz
(http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz).
Regarding dihedrals, the entry regarding the file says that
pdb2gmx cannot
"generate multiple periodic dihedral functions such as CHARMM
uses for some dihedrals -
these must be converted to Ryckaert-Bellemans functions, i.e.
expressed as a cosine power expansion"
This assumption is no longer valid, is it?
As far as I know, infact, now gromacs support multiple periodic
function (funtion 9), is it?
Correct, but with the inclusion of native CHARMM27 in GROMACS, I
have had no reason to upgrade these conversion scripts to support
function type 9.
Mark
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Cordiali saluti, Dr.Oteri Francesco
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