[gmx-users] PRODRG

Fri Feb 11 10:18:31 CET 2011

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.
Thanks in advance
Mohsen

On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul <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>> 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> 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
>>         > > --
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>>         >
>>         >
>>         > --
>>         > Jorge R. Quintero
>>         > Químico
>>         > Universidad Industrial de Santander
>>         > Bucaramanga, Santander - Colombia
>>         >
>>         > --
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>>
>>                 TJ Mustard
>>        Email: 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> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
> --
> ========================================
>
> 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
>
> ========================================
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