Payman Pirzadeh wrote:
Hi again,
I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in
the [atoms ]are specifies as opls_???, doesn't grompp check the database
for the corresponding parameters? Or we should again manually specify the [
atomtypes ] again in either .itp or .top file?
You need to #include "ffoplsaa.itp" to take care of everything related to the
OPLS-AA force field. Invoking grompp is not magic, the topology has to contain
specific instructions for everything you need to handle in your system.
-Justin
Payman
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 10:14 AM
To: [email protected]; 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] making a box of water
OK!
I changed my .top file to
;This is simulation for TIP4P water model
[ defaults ]
; non-bondedtype combrule genpairs FudgeLJ
FudgeQQ N
1 2 NO
; include TIP4P topology
#include "tip4p.itp"
[ system ]
Pure box of water
[ molecules ]
SOL 506
But I still get the same error message! Should I include the [defaults] in
the .itp file?
Payman
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 7:56 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Will #include "ffgmx.itp" solve my problem? Would it be a general solution
or in each case I should specify (if I add other solutes such as
proteins)?
Well, ffgmx is deprecated, so it is probably not the best choice :)
Choosing a
force field should not be a haphazard occasion, it is a very important
choice.
For water models, parameters should be uniform, but if you're simulating a
protein, you'll want to make a very educated decision.
-Justin
Payman
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 7:07 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
You need to #include an appropriate force field that contains the
[defaults],
[atomtypes], etc. before you can define a [moleculetype].
-Justin
Payman Pirzadeh wrote:
Here is my .top file:
;This includes SPC-E potential
#include "spce.itp"
[ system ]
Pure box of water
[ molecules ]
SOL 515
I used the same thing with my own model, but it had worked.
Payman
-----Original Message-----
From: [email protected]
[mailto:[email protected]]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 6:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
I am trying to make a box of water from three different water models. I
can make one from my own water model, but when I want to test TIP4P and
SPCE, as soon as it comes to energy minimization step and using grompp,
I get the following error message:
Program grompp, VERSION 4.0.4
Source code file: topio.c, line: 415
Fatal error:
Syntax error - File spce.itp, line 1
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype
What is the problem causing the code referring to itp file?
See the message I just sent. Something is out of order in your .top
file.
-Justin
Regards,
Payman
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
