[gmx-users] PRODRG

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 11 12:35:57 CET 2011


On 11/02/2011 8:18 PM, mohsen ramezanpour wrote:
> Dear Dr.Justin
>
> I did it,it works.Thanks.
>
> there are another problem:
> I want to add some hydogens to my topology.
> I used ADDHYD atomname,But this dosen't work.
> PLease let me know how can I include some Hydrogenes in my topology.

As Justin suggested, this is not the right forum for PRODRG advice. This 
forum is for GROMACS discussions. I can only suggest you read the PRODRG 
documentation.

Mark

> Thanks in advance
> Mohsen
>
> On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     mohsen ramezanpour wrote:
>
>         Dear Dr.Justin
>
>         I have read this section before.
>         There are 2 problem:
>         1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
>         they result in ERROR in PRODRG
>
>
>     You have to run PRODRG twice.  The first time, you get the wrong
>     output.  Note the atom name that PRODRG assigns to your N atom.
>      The second time, use DELHYD (name).  If that doesn't work, then I
>     have no idea and you're better off submitting your question to the
>     PRODRG developers.
>
>
>         2:Actually I don't know the additional hydrogen is necessary
>         or not!
>         Because it may be necessary for proper protonation.
>         My drug(Sertraline) is in a solvent,it may interact with water
>         molecules and Nitrogen may  get an additional hydrogen.
>
>
>     A doubly-protonated secondary amine would be a fairly strong acid.
>      You should do a pKa calculation to determine what is relevant
>     rather than guessing.  There are web servers and other software
>     out there that can do this for you.  Google is your friend.
>
>     -Justin
>
>         What do you think?
>
>
>
>         On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>            The OP's question is easily answered by referring to the
>         PRODRG FAQ
>            in dealing with proper protonation.
>
>            As for Antechamber and the like, these are good tools, but
>         do not
>            produce GROMOS-compatible topologies, if that is indeed the
>            underlying goal.  We've done thorough analysis of various QM
>            calculation methods for GROMOS charges, and none of them
>         produce
>            completely satisfactory topologies.  Antechamber, Spartan,
>         Gaussian,
>            etc are good for initial charge calculations, but IMHO do not
>            qualify as an "end result" for GROMOS parameterization due
>         to the
>            empirical refinement used in the force field derivation.
>          All of
>            that makes GROMOS parameterization somewhat tricky, and
>         hence why
>            force field choice is so incredibly important when designing
>            projects... ;)
>
>            -Justin
>
>
>            TJ Mustard wrote:
>
>
>
>                Yes I would recommend acpype.
>
>                On February 9, 2011 at 9:42 AM
>         jorge_quintero at ciencias.uis.edu.co
>         <mailto:jorge_quintero at ciencias.uis.edu.co>
>         <mailto:jorge_quintero at ciencias.uis.edu.co
>         <mailto:jorge_quintero at ciencias.uis.edu.co>> wrote:
>
>         > I think that is better to use antechamber tools.
>         >
>         >
>         > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>         > >> Dear Users
>         > >>
>         > >> I am using PRODRG to make topology for my drug
>         > >> It addes Hydrogenes but in wrong way.
>         > >> My Nitrogen atom is bonded to 2 Carbos,
>         > >> and PRODRG addes 2 Hydrogenes to it .
>         > >> Please let me know how can I do.
>         > >> Thanks in advance
>         > >
>         > > This is not really the forum to get help about that. You
>                need to read
>         > > how to PRODRG needs input, and supply something it can deal
>                with. Then
>         > > do a whole bunch more work testing what it produced.
>         > >
>         > > Mark
>         > > --
>         > > gmx-users mailing list gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>
>         > > 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 gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>         <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
>
>         > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>         > >
>         >
>         >
>         > --
>         > Jorge R. Quintero
>         > Químico
>         > Universidad Industrial de Santander
>         > Bucaramanga, Santander - Colombia
>         >
>         > --
>         > gmx-users mailing list gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>
>         > 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 gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>         <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
>
>         > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>         >
>
>                         TJ Mustard
>                Email: mustardt at onid.orst.edu
>         <mailto:mustardt at onid.orst.edu> <mailto:mustardt at onid.orst.edu
>         <mailto:mustardt at onid.orst.edu>>
>
>
>
>            --     ========================================
>
>            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> <http://vt.edu> | (540)
>         231-9080
>
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>            ========================================
>            --     gmx-users mailing list gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>
>         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 gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>         <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
>
>            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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110211/73fcce42/attachment.html>


More information about the gromacs.org_gmx-users mailing list