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

[Andrey V Golovin]

 what does it mean ignore non polar hydrogens?
in what sense do you mean ignore? h-bonding?


NRLF> Hi Freda (??)
NRLF> This e-mail arrived to my inbox. I have forwarded it to gmx mailing list.

NRLF> Nuno

NRLF> ----- Original Message ----- 
NRLF> From: "freda" <xbcd at eyou.com>
NRLF> To: <nunolf at ci.uc.pt>
NRLF> Sent: Thursday, July 29, 2004 8:02 AM
NRLF> Subject: Can you help me ?


>> hi:
>>      I  use the PRODRG to convert a small molecular contained the
NRLF> sulphonic
>> acid, but
>> the PRODRG won't add the hydrogen to the oxgen of sulphnate group, even if
NRLF> 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
NRLF> four
>> words), unfortunatly, it's not effect. The hydrogen of sulphonic acid is
NRLF> not
>> still added.
>>   The structure of this molecule is in the attachment .
>>   The structure information of my molecular is listede as followed :
>> ATOM      1  C1  INR  1298       5.479  42.288  49.591  1.00  0.00
>>
>> ATOM      2  C2  INR  1298       4.474  42.643  50.507  1.00  0.00
>>
>> ATOM      3  C3  INR  1298       3.185  42.041  50.488  1.00  0.00
>>
>> ATOM      4  C4  INR  1298       2.939  41.052  49.489  1.00  0.00
>>
>> ATOM      5  C5  INR  1298       3.962  40.688  48.549  1.00  0.00
>>
>> ATOM      6  C6  INR  1298       5.251  41.307  48.589  1.00  0.00
>>
>> ATOM      7  C8  INR  1298       5.139  43.688  51.353  1.00  0.00
>>
>> ATOM      8  O10 INR  1298       4.608  44.260  52.282  1.00  0.00
>>
>> ATOM      9  C9  INR  1298       6.514  43.828  50.830  1.00  0.00
>>
>> ATOM     10  C11 INR  1298       7.575  44.609  51.186  1.00  0.00
>>
>> ATOM     11  C12 INR  1298       8.895  44.592  50.514  1.00  0.00
>>
>> ATOM     12  O13 INR  1298       9.167  43.886  49.543  1.00  0.00
>>
>> ATOM     13  N14 INR  1298       9.694  45.429  51.104  1.00  0.00
>>
>> ATOM     14  N7  INR  1298       6.596  42.991  49.815  1.00  0.00
>>
>> ATOM     15  C15 INR  1298       7.776  45.632  52.303  1.00  0.00
>>
>> ATOM     16  C20 INR  1298       6.991  46.187  53.355  1.00  0.00
>>
>> ATOM     17  C19 INR  1298       7.591  47.156  54.223  1.00  0.00
>>
>> ATOM     18  C18 INR  1298       8.941  47.558  54.040  1.00  0.00
>>
>> ATOM     19  C17 INR  1298       9.716  47.006  52.984  1.00  0.00
>>
>> ATOM     20  C16 INR  1298       9.111  46.047  52.134  1.00  0.00
>>
>> ATOM     21  S21 INR  1298       6.585  47.819  55.525  1.00  0.00
>>
>> ATOM     22  O24 INR  1298       7.483  48.751  56.254  1.00  0.00
>>
>> ATOM     23  O23 INR  1298       6.190  46.745  56.409  1.00  0.00
>>
>> ATOM     24  O22 INR  1298       5.563  48.627  54.891  1.00  0.00
>>   Could you help me  again? This is very important to my research.
>>     thank you again
>>   A doctor told me "type
>> another line in your gro file and make up some
>> coordinates. Then you can try to modify top/itp file to
>> add one bond, one angle, three dihaedrals and three
>> pairs (or something like that). Then you can restrain
>> the rest of molecule and minimize it. Newertheless,
>> customization of force field and calculation of charges
>> remains an issue."
>>   I want to gaussian calculate the charge.
>>   I have a question : If my ligand .itp file contains all hydrogen, not
NRLF> only
>> polar
>> hydrogen, my protein  .top file is produced in the gromacs forcefied,
NRLF> could I
>> add the ligand .itp file to the protein .top file? Does the calculation
NRLF> ignore
>> the non-polar hydrogen ?
>>  than you


-- 
Best regards,
 Andrey                            mailto:golovin at genebee.msu.su