[gmx-users] gromos function type assigned by grompp
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 8 01:46:07 CEST 2008
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" <jalemkul at vt.edu>:
>>
>>> Quoting Romelia Salomon <romelia at caltech.edu>:
>>>
>>>> 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 at 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 gmx-users-request at gromacs.org.
>>>>> 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
>>> jalemkul at vt.edu | (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
>> jalemkul at vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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 gmx-users-request at gromacs.org.
>> 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
========================================
More information about the gromacs.org_gmx-users
mailing list