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?
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 _______________________________________________ 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 _______________________________________________ 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
