Okay, thanks, I'll stick to Amber then. Thanks again, Majid
________________________________ From: Justin A. Lemkul <[email protected]> To: Gromacs Users' List <[email protected]> Sent: Sun, April 17, 2011 6:35:07 PM Subject: Re: [gmx-users] .top file for DNA-CNT majid hasan wrote: > Okay, so I just removed #include forcefield from top, and [system] [molecule] >directives from the bottom of my topology file, and saved it as .itp file. Is >that fine? > Yes. > And, if I #include water topology in dna.itp file, then I shouldn't include > it >in system's topology file, and it doesn't make any difference whether I >include >water in a molecule.itp file or I add it explicitly in system topology, right? > Correct. I often find it much simpler to just #include everything in one .top file rather than having unnecessary nested #includes, but do what makes the most sense for yourself. > Moreover, I created cnt.top using oplsaa forcefield, so in my cnt.itp file >carbon atoms' "type" is opls_240. So when I run the grompp using >amber99sb-ildn, >it gives me the following error: Fatal Error: Atomtype opls_240 not found, >which >is probably because amber doesn't recognize opls_240. > Never mix and match force fields. You must have one self-consistent representation of the system. > How should I correct the atom type in my cnt.itp file? If I just add an >atomtype opls_240 in /amber99sb-ildn.ff/atomtypes.atp, would it be enough? >Manual's section 5.8.3 says that "after definition of new atom > No. You can't simply append one force field's content to another and hope it works. You may be able to form a syntactically correct force field, but it would be a complete hack job that would not give anything close to a reliable simulation. > types, additional non-bonded, and pair parameters can be defined." I earlier >added some CNT parameters ([bond types], [angle types], ..) in >ffoplsaabon.itp, >do I need to make exactly the same changes in amber.ff/ffbonded.itp? > Leave these files alone. There is no need to alter them in this case. > Is it generally not possible to create topology of one molecule using one >forcefield, and then do MD simulation of entire system using another >forcefield >(without changing parameters etc.)? > In general, no, force fields cannot be combined in this way. There are limited exceptions, but this case is not one of them. You need to choose a parent force field that is suitable for all components of your system and derive molecule topologies from this force field. Mixing and matching will be a great way to waste time. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin > Thanks for your help, > Majid > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <[email protected]> > *To:* Discussion list for GROMACS users <[email protected]> > *Sent:* Sun, April 17, 2011 4:54:11 PM > *Subject:* Re: [gmx-users] .top file for DNA-CNT > > > > majid hasan wrote: > > Dear All, > > > > I want to simulate DNA-CNT interaction, and reproduce the helical wrapping >of DNA around CNT in the first step, and later study the effects of >temperature, >CNT length etc on the favorable geometries of hybrid. > > > > I have created .top files for DNA, and CNT separately. To generate the top >file of entire system (DNA-CNT), I added CNT in a box with DNA using genbox. >But >when I try to create .top file using pdb2gmx and Amber forcefield, I get an >error that atom C in residue 11 C not found in rtp entry because rtp because >.rtp file in Amber only contain dna residues, and if I use some other >forcefield >like oplsaa then dna residues won't be present. So how do I create the .top >file >for whole system i.e DNA-CNT? > > > > Mailing list suggests that another and probably easier way of doing this > is >to create .itp file for CNT, and add it to dna.top file using #include file >mechanism. So I wanted to ask how can I create .itp file from topology file >(because I have the toplogy file for CNT), or do I need to create it manually >from scratch? > > > > The conversion of .top to .itp is simple. A .top is a system topology and >contains a description of the entire system. An .itp file describes one type >of >molecule. To create a .itp from a .top, follow this: > > http://www.gromacs.org/Documentation/File_Formats/.itp_File > > Then a simple system topology is just: > > #include (whatever force field) > #include "cnt.itp" > #include "dna.itp" > #include "spc.itp" (or whatever water) > #include "ions.itp" (if needed) > > Finish with appropriate [system] and [molecules] directives. > > -Justin > > > Thank You, > > Majid > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
