[gmx-users] Topology

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 10 13:04:09 CET 2010



teklebrh at ualberta.ca wrote:
> Dear Justin,
> 
> First of all thank you for your help..
> 
> I have developed the toplogy file for my molecule using the PRODRG 
> server. But the topology did not include properly the carboxylic acid 
> functional group ( with proton) instead the software assumes both 
> oxygens as identical due to resonance. Therefore I want to modify my 
> topology .....what do I need to do.
> 

 From the PRODRG FAQ:

"Q: PRODRG doesn't properly protonate my molecule.
A: This can be fixed by adding the command

ADDHYD atomname

or

DELHYD atomname

to your input drawing/PDB file."

No need to hack the topology.  Run PRODRG once to identify which atom name it 
will assign to the oxygens, then follow the instructions above.

-Justin

> In side my topology (initial)
> ===========================================================
> 44 CH1 1 UNK CA    13    0.143    13.0190
> 45 C   1 UNK C     13    0.372    12.0110
> 46 OM 1  UNK OXT   13    -0.757   15.9994
> 47 OM 1  UNK O     13    -0.758   15.9994
> ============================================================
> 
> MODIFIED to the following topology
> ============================================================
> 44 CH1 1 UNK CA    13   XXX     13.0190
> 45 C   1 UNK C     13   XXX     12.0110
> 46 O   1 UNK OXT   13   XXX     15.9994
> 47 OA  1 UNK O     13   XXX     15.9994
> 48 HO  1 UNK HAA   13   XXX     1.00800
> 
> ===========================================================
> 
> XXX refers to a charge of each ......
> How can I allocate a charge distribution for each united atom molecule 
> in the modified topology .......
> 
> Remark
> 
> I checked the .RTP file and I have found the following information for the
> [ ASPH] residue ....
> 
>    CG     C     0.53000     2
>   OD1     O    -0.38000     2
>   OD2    OA    -0.54800     2
>   HD2    HO     0.39800     2
> 
> But in this case eventhough this describes for the carboxilic acid 
> functional group . It does not include CH1 in the same group...... what 
> do I need to do to
> 
> Example
>   CA     CH1   XXXXXXX     2
>   CG     C     0.53000     2
>   OD1     O    -0.38000     2
>   OD2    OA    -0.54800     2
>   HD2    HO     0.39800     2
> 
> XXXXXX is the new charge for CH1 which I do not know..... can you 
> help..... or simply I have to put 0.00000
> 
> have a great day
> 
> Rob
> 
> ***************************************************
> The entire Topology is the following
> 
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CH3     1  UNK     CAZ     1    0.000  15.0350
>      2       CH2     1  UNK     CAK     1    0.000  14.0270
>      3       CH2     1  UNK     CBS     2    0.000  14.0270
>      4       CH2     1  UNK     CBL     2    0.000  14.0270
>      5       CH2     1  UNK     CBG     3    0.000  14.0270
>      6       CH2     1  UNK     CBM     3    0.000  14.0270
>      7       CH1     1  UNK     CBA     3    0.000  13.0190
>      8       CH2     1  UNK     CBD     3    0.000  14.0270
>      9       CH2     1  UNK     CBE     3    0.000  14.0270
>     10       CH2     1  UNK     CBF     4    0.000  14.0270
>     11       CH2     1  UNK     CBJ     4    0.000  14.0270
>     12       CH2     1  UNK     CBN     5    0.101  14.0270
>     13       CH3     1  UNK     CBT     5    0.057  15.0350
>     14      NR6*     1  UNK     NBU     5    0.069  14.0067
>     15        CB     1  UNK     CBP     5    0.346  12.0110
>     16         O     1  UNK     OCB     5   -0.573  15.9994
>     17        CB     1  UNK     CAG     6    0.351  12.0110
>     18         O     1  UNK     OCA     6   -0.565  15.9994
>     19       CH1     1  UNK     CBI     6    0.178  13.0190
>     20      CR61     1  UNK     CBO     6    0.018  13.0190
>     21      CR61     1  UNK     CAV     6    0.018  13.0190
>     22        CB     1  UNK     CAN     7    0.000  12.0110
>     23        CB     1  UNK     CAR     7    0.000  12.0110
>     24        CB     1  UNK     CAX     8    0.000  12.0110
>     25        CB     1  UNK     CBC     8    0.000  12.0110
>     26      CR61     1  UNK     CBH     8    0.000  13.0190
>     27      CR61     1  UNK     CAW     8    0.000  13.0190
>     28       CH1     1  UNK     CAQ     9    0.074  13.0190
>     29        CB     1  UNK     CAM     9    0.001  12.0110
>     30      CR61     1  UNK     CAU     9   -0.037  13.0190
>     31      CR61     1  UNK     CAI     9   -0.038  13.0190
>     32        CB     1  UNK     CAC    10    0.003  12.0110
>     33        CB     1  UNK     CAE    10    0.442  12.0110
>     34         O     1  UNK     OBX    10   -0.448  15.9994
>     35        CB     1  UNK     CAB    10    0.003  12.0110
>     36        CB     1  UNK     CAF    11    0.004  12.0110
>     37        CB     1  UNK     CAJ    11    0.004  12.0110
>     38      CR61     1  UNK     CAP    11   -0.008  13.0190
>     39      CR61     1  UNK     CAH    12   -0.013  13.0190
>     40        CB     1  UNK     CAA    12    0.003  12.0110
>     41        CB     1  UNK     CAD    12    0.411  12.0110
>     42         O     1  UNK     OBW    12   -0.483  15.9994
>     43      NR6*     1  UNK       N    12    0.082  14.0067
> 
>     44       CH1     1  UNK      CA    13    0.143  13.0190
>     45         C     1  UNK       C    13    0.372  12.0110
>     46        OM     1  UNK     OXT    13   -0.757  15.9994
>     47        OM     1  UNK       O    13   -0.758  15.9994
> 
>     48       CH2     1  UNK      CB    14    0.068  14.0270
>     49        CB     1  UNK      CG    14    0.002  12.0110
>     50      CR61     1  UNK     CD1    14   -0.023  13.0190
>     51      CR61     1  UNK     CE1    14   -0.024  13.0190
>     52      CR61     1  UNK      CZ    14   -0.023  13.0190
>     53      CR61     1  UNK     CE2    15    0.000  13.0190
>     54      CR61     1  UNK     CD2    15    0.000  13.0190
> 
> 
> 

-- 
========================================

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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