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? 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 >> > > >> > > ======================================== >> > > _______________________________________________ >> > > gmx-users mailing list gmx-users@gromacs.org >> > > 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 >> > > >> > >> > >> > -- >> > **************************************** >> > 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 gmx-users@gromacs.org > 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 > -- **************************************** Romelia Salomon Miller Group 316 Noyes Chemistry Department Caltech _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
