Romelia Salomon wrote:
Ok, for my ligand I was using the Dundee PRODRG Server and the file
produced reads like this for example:
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; CAB CAE
2 3 1 0.139 418400.0 0.139 418400.0 ; CAE CAD
3 4 1 0.139 418400.0 0.139 418400.0 ; CAD CAC
4 5 1 0.153 334720.0 0.153 334720.0 ; CAC CAA
....
I was under the impression this site would be using GROMOS as the
forcefield, and actually the parameters do match the ones found in the
files share/top/ffgmx*.itp, would that be a bug from the website?
No, there's no bug, you've just said it - the parameters come from ffgmx! The
PRODRG server was originally for use with Gromos87-derived parameters. If
you're interested in using Gromos96 topologies (the 43a1 parameter set), you're
better off using PRODRG2.5 at:
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta
-Justin
Thanks about your comments on what to keep in mind when using this
program, it'll save me some problems :)
Cheers,
Romelia
Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
Quoting Romelia Salomon <[EMAIL PROTECTED]>:
Hi Justin
thanks for your email, yes I used the -pp option to print out the file
I
showed here. I am using gromacs-3.3.3 and I compiled it just doing the
typical ./configure make make install and I checked and it's using cc
as a
compiler.
What I was trying to do is to run a calculation using Gromos
forcefield in
another program I have and I was trying to debug it by trying to match
the
energy coming from gromacs using that same forcefield. I tried the -pp
option in grompp to show explicitly the parameters being used during
the
calculation and that is how I got the file I showed. I tried the
gmxdump
and that seems to be ok. I wrote my conversion file based on that file
so
now it works fine :).
Just one last question, in the PRODRG website the gromacs topology
files
generated have function 1 for both angles and bonds, that means that
the
functions to be used are the regular harmonic form for both, right?
Yes, if you're using the ffgmx force field. Beware of doing so! The
manual,
the listing in pdb2gmx, and countless posts on this list warn that ffgmx
is
old
and deprecated. If you are indeed trying to use a Gromos96 parameter
set, be
sure you're calling the right force field!
Also note that PRODRG topologies often require refinement of (at the
very
least)
charges and charge groups. Just something to keep in mind.
-Justin
Thanks a lot for your time!!!
Romelia
Romelia Salomon wrote:
Hi
I am trying to set a calculation based on the GROMOS force field in
a
program I have and I am using GROMACS to generate the (starting)
input
files for me. From reading the manual I know that GROMOS uses a
fourth
power potential (type 2) for bonds and a cosine based angle
potential
(type 2), but I noticed that when using grompp to include the
values for
the parameters explicitly it changes the type from 2 to 1, for
example:
topology file before grompp
[ bonds ]
; ai aj funct c0 c1 c2
c3
1 2 2 gb_2
1 3 2 gb_2
1 4 2 gb_2
1 5 2 gb_20
5 6 2 gb_26
5 10 2 gb_26
after using grompp
This would be from the -pp flag of grompp?
[ bonds ]
; ai aj tp parameters
N H1 1 0.1 1.87e+07
N H2 1 0.1 1.87e+07
N H3 1 0.1 1.87e+07
N CA 1 0.147 8.71e+06
CA CB 1 0.153 7.15e+06
CA C 1 0.153 7.15e+06
Which version of Gromacs are you using? I'm using 3.3.3, and mine
works
just
fine (bond type is 2). Furthermore, it's odd that grompp is
including
atom
names instead of numbers...unless you've interpreted what the output
really is
and transcribed it differently :)
If grompp is changing these, then perhaps it's a bug. Note that
weird
behavior
arises when Gromacs is compiled with gcc 4.1.x, as has been beaten
to
death on
this list :) Without knowing more about your system, this is pure
speculation
and may not be worth anything.
Is this right? Also, for clarification, I know Gromacs uses kj/mol
and
nm
as units, so does that mean that the values included in the ff*.itp
files
under the share/top/ directory are in those units?
The units are all consistent.
-Justin
Also I noticed that the .itp files for bonding interactions in
gmxbon.itp
have declared a type 1 function which would be the regular harmonic
one.
Sorry for the very basic questions, but I wanted to be certain
about
this
things, thanks!!
Romelia
Thanks!
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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--
****************************************
Romelia Salomon
Miller Group
316 Noyes
Chemistry Department
Caltech
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.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
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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 [email protected]
http://www.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
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