[gmx-users] Fw: Can you help me ?

[Anton Feenstra]

Nuno R. L. Ferreira wrote:
> ----- Original Message ----- 
> From: "freda" <xbcd at eyou.com>
> 
>>hi:
>>     I  use the PRODRG to convert a small molecular contained the sulphonic acid, but
>>the PRODRG won't add the hydrogen to the oxgen of sulphnate group, even if I
> 
>>add the hydrogen to the oxgen,the PRODRG will delete it.
>>    I  added  thr order "ADDHYD oxyg"(the length of atomname is not more four
>>words), unfortunatly, it's not effect. The hydrogen of sulphonic acid is not still added.

I don't use ProDrg myself, but I could guess that you need to specify
the actual atom name, like 'O23', in stead of 'oxyg'.

>>  I have a question : If my ligand .itp file contains all hydrogen, not only polar
>>hydrogen, my protein  .top file is produced in the gromacs forcefied, could I
>>add the ligand .itp file to the protein .top file? Does the calculation
> ignore the non-polar hydrogen ?

No, Gromacs will not ignore anything that you have put in your .top/.itp files.
However, you do need to consider the consistency of your molecule with
respect to the rest of the forcefield you are using. If you use the gromacs
forcefield, there are no aliphatic hydrogens in your protein, and you will
have to decide if it makes sense to add aliphatic hydrogens to your molecule.

(By the way, the Gromacs forcefield 'ffgmx' is depricated. You should really
consider using, e.g., the Gromos forcefield 'ffG43a1'.)



-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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