Oh!! thanks!!... gromos, gromacs... that little x escaped my attention :) That should solve all my doubts, thanks a lot!!
Romelia > > > Romelia Salomon wrote: >> 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? >> > > No, there's no bug, you've just said it - the parameters come from ffgmx! > The > PRODRG server was originally for use with Gromos87-derived parameters. If > you're interested in using Gromos96 topologies (the 43a1 parameter set), > you're > better off using PRODRG2.5 at: > > http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta > > -Justin > >> 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 >>> >> >> > > -- > ======================================== > > 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 _______________________________________________ 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
