Jacob Harvey wrote:
Justin,
How do I go about running topolgen on a linux system? There doesn't seem
to be instructions for use, but I'm not familiar with perl scripts. Also
I'd just like to say thank you for all your help. You've been really
good with responding to my e-mail. I know that you have referenced
chapter 5 in the manual multiple times, and I can assure you that I have
read that chapter several times. I am a first year graduate student who
is very new to molecular dynamics so some of the material is not trivial
to me. Thank you again!
To execute:
perl topolgen.pl input.pdb
Guess I forgot to include that in the README; my mistake. I'm working on making
the script better, so I'll update that for a future release. Also be warned
that I have not extensively tested the script beyond some basic small molecules.
Please run some test simulations before collecting any real data.
There are also a number of tutorials on the Gromacs wiki. The one written by
Tsjerk is especially good at diagramming the flow of the programs, input/output,
and how everything is put together. If you are unfamiliar with Gromacs, try out
some tried-and-true methodology on known systems before simulating some bizarre
system. It will save you a lot of headaches.
-Justin
Jacob Harvey
On Sat, Apr 4, 2009 at 3:17 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Jacob Harvey wrote:
Thank you for your help Justin. I have corrected my naming
problem in the pdb file. However, I am still getting errors. It
does not seem to recognize the residues. BUT I dont actually
have "residues" in my system, because I am not modeling a
protein. So I am not sure what to put in the residue name
column. Gromacs does work on molecules that are not proteins
correct? My molecules are histidine like so I tried putting HIS
as the residue name, but I got the error:
If you want to use pdb2gmx to automatically generate your topology,
you have to ensure that the appropriate .rtp entry is present within
the desired force field and has the same name as the building block
you are trying to use (again, this is spelled out in Chapter 5 of
the manual). If you call your molecule "HIS," then pdb2gmx will not
magically build a random molecule; it will try to build histidine,
based on the [ HIS ] entry in the .rtp file, so it will look for the
exact atomic entries for histidine, no more no less.
If you want a topology for an arbitrary molecule, you *can not* use
pdb2gmx (unless you build the .rtp entry yourself). You will have
to build it by hand, or use another program to build the .top file.
I just uploaded a script I wrote to build an OPLS-AA topology from
a .pdb file to the Users Contributions section on the website, but
it does not assign atom types or charges (yet); it is up to you to
assign the parameters and verify them.
"Fatal error:
Residue 'H' not found in residue topology database"
Because it is not histidine.
When I dont put anything in that column I get the error:
"Fatal error:
Residue '' not found in residue topology database"
Because of a formatting error (the fact that your residue is either
blank, or the number 2).
And when I just generically call everything solvent and put SOL
in that column I get:
"Fatal error:
Residue 'S' not found in residue topology database"
Probably another formatting issue. But none of the above actually
solve your problem, you're just trying to fool pdb2gmx into being
magic, which it is not.
-Justin
You get the picture here. Does anyone have any solutions to my
residue naming problem? Thank you.
here is my pdb file:
HETATM 1 CT 2 -4.438 3.334 2.988
HETATM 2 CT 2 0.588 3.313 0.517
HETATM 3 CT 2 5.476 3.310 -2.216
HETATM 4 HC 2 -4.134 2.590 3.731
HETATM 5 HC 2 -5.525 3.438 3.047
HETATM 6 HC 2 -3.996 4.291 3.276
HETATM 7 HC 2 1.480 3.111 1.117
HETATM 8 HC 2 -0.266 3.349 1.200
HETATM 9 HC 2 0.702 4.307 0.076
HETATM 10 HC 2 6.375 3.525 -1.633
HETATM 11 HC 2 4.648 3.862 -1.761
HETATM 12 HC 2 5.628 3.709 -3.223
HETATM 13 CT 2 -3.996 2.922 1.581
HETATM 14 HC 2 -2.902 2.862 1.545
HETATM 15 HC 2 -4.281 3.703 0.865
HETATM 16 CT 2 0.394 2.242 -0.557
HETATM 17 HC 2 -0.485 2.486 -1.167
HETATM 18 HC 2 1.250 2.252 -1.242
HETATM 19 CT 2 5.188 1.805 -2.247
HETATM 20 HC 2 6.018 1.286 -2.742
HETATM 21 HC 2 4.300 1.615 -2.864
HETATM 22 CT 2 -4.587 1.582 1.127
HETATM 23 HC 2 -5.682 1.638 1.161
HETATM 24 HC 2 -4.298 0.792 1.828
HETATM 25 CT 2 0.235 0.836 0.028
HETATM 26 HC 2 -0.616 0.818 0.720
HETATM 27 HC 2 1.117 0.581 0.625
HETATM 28 CT 2 4.981 1.206 -0.852
HETATM 29 HC 2 4.152 1.720 -0.350
Jacob Harvey
On Sat, Apr 4, 2009 at 2:29 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Jacob Harvey wrote:
Dear All,
I am trying to use the OPLS-AA force field to model some
imidazole containing compounds. I've noticed that imidazole
units are referenced in the ffoplsaa.atp file as the
following:
opls_557 14.00670 ; N1 in imidazole
opls_558 12.01100 ; C2 in imidazole
opls_559 14.00670 ; N3 in imidazole
opls_560 12.01100 ; C4 in imidazole
opls_561 12.01100 ; C5 in imidazole
opls_562 1.00800 ; H1 in imidazole
opls_563 1.00800 ; H2 in imidazole
opls_564 1.00800 ; H4 in imidazole
opls_565 1.00800 ; H5 in imidazole
But there are no parameters for these atoms in the
ffoplsaa.rtp
file. Does anyone know how I can go about naming these
atoms in
my pdb file? Thank you in advance.
Not every compound is present in a .rtp file. Check out its
contents and you'll see what it has - pretty much just amino
acids.
The charges on each atom are not specific to an atom type,
they are
specific to a chemical species for which the parameterization
scheme
has been conducted. Lennard-Jones parameters are specified in
ffoplsaanb.itp.
I suggest a thorough read of Chapter 5 of the manual to
understand
the contents of these database-type files, and how they are
used in
assembling a topology.
-Justin
Jacob Harvey
-- --
Jacob Harvey
Graduate Student
University of Massachusetts Amherst
[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[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
www interface or send it to [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[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 www
interface or send it to [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
--
Jacob Harvey
Graduate Student
University of Massachusetts Amherst
[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[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
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[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 www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
--
Jacob Harvey
Graduate Student
University of Massachusetts Amherst
[email protected] <mailto:[email protected]>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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 [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
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
