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

Thu Jul 29 15:57:34 CEST 2004

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

Nuno

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

> 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.
>   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
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 ?
>  than you
>
>
>
>
>
>
>
> --http://www.eyou.com
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>
> --http://vip.eyou.com
> --¿ì¿ìµÇÂ¼ÒÚÓÊVIPÐÅÏä  ×¢²áÄúÖÐÒâµÄÓÃ»§Ãû
>
>
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