[gmx-users] Capping residues

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 8 02:48:09 CEST 2010



Sai Pooja wrote:
> This probably is my ignorance but the error and the "bug" goes when I 
> replaced CBX with NAC everywhere.
> 
> 

I would suggest filing a bugzilla.  I was able to reproduce your problem.  If 
nothing else, pdb2gmx should not be name-specific.  Something very weird is 
going on.  More troubling, the topology that pdb2gmx generated for me with NAC 
as the C-terminal cap had a broken net charge of +0.960 - it appears that 
pdb2gmx is adding double hydrogens to the backbone amides - both H and HN.

With the impending release of Gromacs 4.5, this could be a very problematic bug.

-Justin

> 
> On Wed, Jul 7, 2010 at 6:09 PM, Sai Pooja <saipooja at gmail.com 
> <mailto:saipooja at gmail.com>> wrote:
> 
>     1. I have only added entries in the .rtp files. Do I need to add
>     them in .hdb and .tdb files too? Could I simply define a new
>     terminal in the aminoacids.c.tdb file?
> 
>     For your reference:
> 
>     *Initial PDB file*
>     ATOM      1  C   ACE     1      12.532  -0.094  26.546  1.00  2.10  
>        FR1  C
>     ATOM      2  O   ACE     1      13.443  -0.213  25.696  1.00  1.60  
>        FR1  O
>     ATOM      3  CH3 ACE     1      12.782  -0.027  28.022  1.00  2.17  
>        FR1  C
>     ATOM      4 HH31 ACE     1      13.138  -0.995  28.375  1.00  2.17  
>        FR1  H
>     ATOM      5 HH32 ACE     1      11.856   0.230  28.537  1.00  2.17  
>        FR1  H
>     ATOM      6 HH33 ACE     1      13.535   0.733  28.228  1.00  2.17  
>        FR1  H
>     ATOM      7  N   VAL     2      11.255  -0.021  26.193  1.00  1.60  
>        FR1  N
>     ATOM      8  CA  VAL     2      10.854  -0.210  24.846  1.00  2.37  
>        FR1  C
>     ATOM      9  C   VAL     2      11.022   1.197  24.222  1.00  2.10  
>        FR1  C
>     ATOM     10  O   VAL     2      10.340   2.192  24.528  1.00  1.60  
>        FR1  O
>     ATOM     11  CB  VAL     2       9.401  -0.679  24.711  1.00  2.37  
>        FR1  C
>     ATOM     12  CG1 VAL     2       9.113  -0.953  23.274  1.00  2.17  
>        FR1  C
>     ATOM     13  CG2 VAL     2       9.141  -1.946  25.547  1.00  2.17  
>        FR1  C
>     ATOM     14  H   VAL     2      10.636   0.148  26.935  1.00  0.80  
>        FR1  H
>     ATOM     15  N   GLN     3      12.113   1.241  23.470  1.00  1.60  
>        FR1 
>     ATOM     16  H   GLN     3      12.656   0.425  23.466  1.00  0.80  
>        FR1 
>     ATOM     17  CA  GLN     3      12.533   2.509  22.812  1.00  2.37  
>        FR1 
>     ATOM     18  CB  GLN     3      13.982   2.287  22.560  1.00  2.23  
>        FR1 
>     ATOM     19  CG  GLN     3      14.807   3.474  22.166  1.00  2.23  
>        FR1 
>     ATOM     20  CD  GLN     3      16.219   3.156  22.441  1.00  2.10  
>        FR1 
>     ATOM     21  OE1 GLN     3      16.635   2.341  23.295  1.00  1.60  
>        FR1 
>     ATOM     22  NE2 GLN     3      17.095   3.710  21.642  1.00  1.60  
>        FR1 
>     ATOM     23 HE21 GLN     3      18.031   3.421  21.665  1.00  0.80  
>        FR1 
>     ATOM     24 HE22 GLN     3      16.790   4.446  21.071  1.00  0.80  
>        FR1 
>     ATOM     25  C   GLN     3      11.689   2.846  21.556  1.00  2.10  
>        FR1 
>     ATOM     26  O   GLN     3      11.395   3.988  21.389  1.00  1.60  
>        FR1 
>     ATOM     27  N   LEU     4      11.403   1.872  20.676  1.00  1.60  
>        FR1 
>     ATOM     28  H   LEU     4      11.747   0.959  20.767  1.00  0.80  
>        FR1 
>     ATOM     29  CA  LEU     4      10.606   2.121  19.473  1.00  2.37  
>        FR1 
>     ATOM     30  CB  LEU     4      11.011   1.111  18.398  1.00  2.23  
>        FR1 
>     ATOM     31  CG  LEU     4      12.501   1.073  18.020  1.00  2.37  
>        FR1 
>     ATOM     32  CD1 LEU     4      12.869  -0.185  17.207  1.00  2.17  
>        FR1 
>     ATOM     33  CD2 LEU     4      12.893   2.344  17.332  1.00  2.17  
>        FR1 
>     ATOM     34  C   LEU     4       9.082   2.102  19.484  1.00  2.10  
>        FR1 
>     ATOM     35  O   LEU     4       8.400   1.579  20.374  1.00  1.60  
>        FR1 
>     ATOM     36  N   CBX     5       8.609   2.722  18.430  1.00  1.60  
>        FR1
>     ATOM     37  H   CBX     5       9.198   3.338  17.946  1.00  0.80  
>        FR1
>     ATOM     38 CH3  CBX     5       7.176   2.594  17.895  1.00  2.17  
>        FR1
>     ATOM     39 HH31 CBX     5       6.785   1.605  18.135  1.00  2.17  
>        FR1  H
>     ATOM     40 HH32 CBX     5       7.178   2.732  16.814  1.00  2.17  
>        FR1  H
>     ATOM     41 HH33 CBX     5       6.547   3.355  18.357  1.00  2.17  
>        FR1
> 
> 
>     *Changes in .rtp file*
>     [ ACE ]   
>      [ atoms ]
>             CH3     CT3     -0.270  0
>             HH31    HA      0.090   0
>             HH32    HA      0.090   0
>             HH33    HA      0.090   0
>             C       C       0.510   1
>             O       O       -0.510  1
>      [ bonds ]
>             C       CH3
>             C       +N
>             CH3     HH31
>             CH3     HH32
>             CH3     HH33
>             O       C
>      [ impropers ]
>             C       CH3     +N      O
>     [ CBX ]
>      [ atoms ]
>            N       NH1     -0.470  1 
>            HN      H       0.310   1 
>            CH3     CT3     -0.110  1 
>            HH31    HA      0.090   1 
>            HH32    HA      0.090   1 
>            HH33    HA      0.090   1 
>      [ bonds ]
>            -C      N
>            N       HN
>            N       CH3
>            CH3     HH31
>            CH3     HH32
>            CH3     HH33
>      [ impropers ]
>            N       -C      CH3     HN
>            -C      CH3     N       -O
> 
>     *command:*
>     pdb2gmx -f F1.pdb -q F1clean.pdb -nocmap -v -ss -ter -o work.gro -p
>     work.top
> 
>     *.gro file from pdb2gmx*
>     1ACE    CH3    1   1.278  -0.003   2.802
>         1ACE   HH31    2   1.314  -0.100   2.838
>         1ACE   HH32    3   1.186   0.023   2.854
>         1ACE   HH33    4   1.354   0.073   2.823
>         1ACE      C    5   1.253  -0.009   2.655
>         1ACE      O    6   1.344  -0.021   2.570
>         2VAL      N    7   1.125  -0.002   2.619
>         2VAL     HN    8   1.064   0.015   2.694
>         2VAL     CA    9   1.085  -0.021   2.485
>         2VAL     HA   10   1.142  -0.094   2.447
>         2VAL     CB   11   0.940  -0.068   2.471
>         2VAL     HB   12   0.879   0.005   2.503
>         2VAL    CG1   13   0.911  -0.095   2.327
>         2VAL   HG11   14   0.817  -0.126   2.318
>         2VAL   HG12   15   0.925  -0.012   2.274
>         2VAL   HG13   16   0.973  -0.167   2.294
>         2VAL    CG2   17   0.914  -0.195   2.555
>         2VAL   HG21   18   0.819  -0.223   2.544
>         2VAL   HG22   19   0.974  -0.268   2.523
>         2VAL   HG23   20   0.932  -0.175   2.651
>         2VAL      C   21   1.102   0.120   2.422
>         2VAL      O   22   1.034   0.219   2.453
>         3GLN      N   23   1.211   0.124   2.347
>         3GLN     HN   24   1.266   0.043   2.347
>         3GLN     CA   25   1.253   0.251   2.281
>         3GLN     HA   26   1.240   0.331   2.340
>         3GLN     CB   27   1.398   0.229   2.256
>         3GLN    HB1   28   1.437   0.191   2.340
>         3GLN    HB2   29   1.406   0.161   2.183
>         3GLN     CG   30   1.481   0.347   2.217
>         3GLN    HG1   31   1.469   0.367   2.119
>         3GLN    HG2   32   1.453   0.428   2.270
>         3GLN     CD   33   1.622   0.316   2.244
>         3GLN    OE1   34   1.663   0.234   2.329
>         3GLN    NE2   35   1.709   0.371   2.164
>         3GLN   HE21   36   1.803   0.342   2.167
>         3GLN   HE22   37   1.679   0.445   2.107
>         3GLN      C   38   1.169   0.285   2.156
>         3GLN      O   39   1.140   0.399   2.139
>         4LEU      N   40   1.140   0.187   2.068
>         4LEU     HN   41   1.175   0.096   2.077
>         4LEU     CA   42   1.061   0.212   1.947
>         4LEU     HA   43   1.085   0.309   1.937
>         4LEU     CB   44   1.101   0.111   1.840
>         4LEU    HB1   45   1.076   0.020   1.873
>         4LEU    HB2   46   1.049   0.133   1.757
>         4LEU     CG   47   1.250   0.107   1.802
>     4LEU     HG   48   1.305   0.103   1.886
>         4LEU    CD1   49   1.287  -0.019   1.721
>         4LEU   HD11   50   1.384  -0.017   1.699
>         4LEU   HD12   51   1.267  -0.100   1.775
>         4LEU   HD13   52   1.234  -0.020   1.636
>         4LEU    CD2   53   1.289   0.234   1.733
>         4LEU   HD21   54   1.386   0.231   1.709
>         4LEU   HD22   55   1.235   0.246   1.650
>         4LEU   HD23   56   1.273   0.312   1.794
>         4LEU      C   57   0.908   0.210   1.948
>         4LEU    OT1   58   0.840   0.158   2.037
>         4LEU    OT2   59   0.845   0.235   1.830
>         4LEU    HT2   60   0.746   0.231   1.844
>         5CBX      N   61   0.861   0.272   1.843
>         5CBX     HN   62   0.920   0.334   1.795
>         5CBX    CH3   63   0.718   0.259   1.789
>         5CBX   HH31   64   0.678   0.161   1.814
>         5CBX   HH32   65   0.718   0.273   1.681
>         5CBX   HH33   66   0.655   0.336   1.836
>        1.14840   0.71270   1.21755
> 
> 
> 
> 
> 
> 
>     *PDB file from pdb2gmx using -q option*
> 
>     TITLE     Gromacs Runs On Most of All Computer Systems
>     MODEL        1
>     ATOM      1  C   ACE     1      12.532  -0.094  26.546  1.00  2.10  
>             C
>     ATOM      2  O   ACE     1      13.443  -0.213  25.696  1.00  1.60  
>             O
>     ATOM      3  CH3 ACE     1      12.782  -0.027  28.022  1.00  2.17  
>             C
>     ATOM      4 1HH3 ACE     1      13.138  -0.995  28.375  1.00  2.17  
>             H
>     ATOM      5 2HH3 ACE     1      11.856   0.230  28.537  1.00  2.17  
>             H
>     ATOM      6 3HH3 ACE     1      13.535   0.733  28.228  1.00  2.17  
>             H
>     ATOM      7  N   VAL     2      11.255  -0.021  26.193  1.00  1.60  
>             N
>     ATOM      8  CA  VAL     2      10.854  -0.210  24.846  1.00  2.37  
>             C
>     ATOM      9  C   VAL     2      11.022   1.197  24.222  1.00  2.10  
>             C
>     ATOM     10  O   VAL     2      10.340   2.192  24.528  1.00  1.60  
>             O
>     ATOM     11  CB  VAL     2       9.401  -0.679  24.711  1.00  2.37  
>             C
>     ATOM     12  CG1 VAL     2       9.113  -0.953  23.274  1.00  2.17  
>             C
>     ATOM     13  CG2 VAL     2       9.141  -1.946  25.547  1.00  2.17  
>             C
>     ATOM     14  H   VAL     2      10.636   0.148  26.935  1.00  0.80  
>             H
>     ATOM     15  N   GLN     3      12.113   1.241  23.470  1.00  1.60  
>             N
>     ATOM     16  H   GLN     3      12.656   0.425  23.466  1.00  0.80  
>             H
>     ATOM     17  CA  GLN     3      12.533   2.509  22.812  1.00  2.37  
>             C
>     ATOM     18  CB  GLN     3      13.982   2.287  22.560  1.00  2.23  
>             C
>     ATOM     19  CG  GLN     3      14.807   3.474  22.166  1.00  2.23  
>             C
>     ATOM     20  CD  GLN     3      16.219   3.156  22.441  1.00  2.10  
>             C
>     ATOM     21  OE1 GLN     3      16.635   2.341  23.295  1.00  1.60  
>             O
>     ATOM     22  NE2 GLN     3      17.095   3.710  21.642  1.00  1.60  
>             N
>     ATOM     23 1HE2 GLN     3      18.031   3.421  21.665  1.00  0.80  
>            HE
>     ATOM     24 2HE2 GLN     3      16.790   4.446  21.071  1.00  0.80  
>            HE
>     ATOM     25  C   GLN     3      11.689   2.846  21.556  1.00  2.10  
>             C
>     ATOM     26  O   GLN     3      11.395   3.988  21.389  1.00  1.60  
>             O
>     ATOM     27  N   LEU     4      11.403   1.872  20.676  1.00  1.60  
>             N
>     ATOM     28  H   LEU     4      11.747   0.959  20.767  1.00  0.80  
>             H
>     ATOM     29  CA  LEU     4      10.606   2.121  19.473  1.00  2.37  
>             C
>     ATOM     30  CB  LEU     4      11.011   1.111  18.398  1.00  2.23  
>             C
>     ATOM     31  CG  LEU     4      12.501   1.073  18.020  1.00  2.37  
>             C
>     ATOM     32  CD1 LEU     4      12.869  -0.185  17.207  1.00  2.17  
>             C
>     ATOM     33  CD2 LEU     4      12.893   2.344  17.332  1.00  2.17  
>             C
>     ATOM     34  C   LEU     4       9.082   2.102  19.484  1.00  2.10  
>             C
>     ATOM     35  O   LEU     4       8.400   1.579  20.374  1.00  1.60  
>             O
>     ATOM     36  N   CBX     5       8.609   2.722  18.430  1.00  1.60  
>             N
>     ATOM     37  H   CBX     5       9.198   3.338  17.946  1.00  0.80  
>             H
>     ATOM     38  CH3 CBX     5       7.176   2.594  17.895  1.00  2.17  
>             C
>     ATOM     39 1HH3 CBX     5       6.785   1.605  18.135  1.00  2.17  
>             H
>     ATOM     40 2HH3 CBX     5       7.178   2.732  16.814  1.00  2.17  
>             H
>     ATOM     41 3HH3 CBX     5       6.547   3.355  18.357  1.00  2.17  
>             H
>     TER
>     ENDMDL
> 
> 
>     These files were generated using the option -COOH for C terminal.
>     *However, if "none" is chosen, I get the error:*
> 
>     Fatal error:
>       There is a dangling bond at at least one of the terminal ends.
>       Select a proper terminal entry.
>       For more information and tips for troubleshooting, please check the
>       GROMACS
>        I have used Mark's definitions for capping residues in the rtp file.
> 
> 
>     Pooja
> 
> 
>     On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>         Sai Pooja wrote:
> 
>             I checked again and the error does not go. Please read the
>             steps below.
> 
>             The pdb file I started off with did not have any hydrogens.
>             However, the way I had specified the capping residues in the
>             .rtp file (SEE MARK'S MAIL), I had to specify hydrogens in
>             the pdb file for the capping residues. So I used pymol to
>             add hydrogens to my pdb file. I then used this file with
>             charmm force field. However, pymol had added hydrogens
>             everywhere and this was different from the definition of the
>             standard residues defined in the .rtp file. I could not
>             directly use -ignh because I needed the hydrogens for the
>             capping residues. So I created a file that contained the
>             hydrogens on the capping residues only. This resolved the
>             error related to hydrogens.
> 
> 
>         Probably an easier and more reliable approach would simply be to
>         create an .hdb entry for your capping groups.
> 
> 
> 
>             Error-from previous mail-NOT RESOLVED
>             (Fatal error:
>               There is a dangling bond at at least one of the terminal ends.
>               Select a proper terminal entry.
>               For more information and tips for troubleshooting, please
>             check the
>               GROMACS
>                I have used Mark's definitions for capping residues in
>             the rtp file.
> 
>               In the pdb file, this is what the capping residues look like:
> 
>               ATOM     33  N   CBX     5       8.609   2.722  18.430
>              1.00  1.60         FR1
>               ATOM     34  H   CBX     5       9.198   3.338  17.946
>              1.00  0.80         FR1
>               ATOM     35 CH3  CBX     5       7.176   2.594  17.895
>              1.00  2.17         FR1
> 
> 
>         Maybe this is just showing up incorrectly in my mail client, but
>         I wonder if that CH3 is somehow misaligned and therefore not
>         correctly identified.  I presume that you changed the residue
>         name in the .rtp file accordingly?  I suppose the error message
>         would be different (something like "residue not found") but I
>         just want to make sure.  Mark's entry used NAC.
> 
> 
>               ATOM      1  CH3 ACE     1      12.782  -0.027  28.022
>              1.00  2.17         FR1
>               ATOM      2  C   ACE     1      12.532  -0.094  26.546
>              1.00  2.10         FR1
>               ATOM      3  O   ACE     1      13.443  -0.213  25.696
>              1.00  1.60         FR1 )
> 
>             The error stated in the previous mail(quoted above) occurred
>             when I chose "none" for the both terminals or the carboxylic
>             terminal option (using -ter). It worked fine if I chose
>             "none" at the N terminal and any other option except "none"
>             at the carboxylic acid terminal. So I chose "none" at N
>             terminal and some option randomly at the carboxylic acid
>             terminal. As expected, it adds a terminal at that end of the
>             residue before my capping residue which is something I DONT
>             want. I
> 
> 
>         So does pdb2gmx somehow add the C-terminal cap after the
>         carboxylate terminus?
> 
> 
>             havent been able to find a way around it. Interestingly,
>             when I generate a pdb file using -q, and open that pdb file
>             in pymol, I dont get the terminal carboxylic acid that
>             pdb2gmx gives in the .gro file.
> 
> 
>         So the cap is applied properly in that structure?
> 
> 
>             I am not sure how to correct this. One way would be to
>             remove those entries from the final .gro and .top file but
>             not sure if that would be right.
> 
> 
>         This all sounds very fishy.  This may be worth a bugzilla entry,
>         but only if you can build the structure in a very sound way,
>         probably using .hdb entries (or an appropriate all-atom
>         structure, which you've yet to demonstrate).
> 
>         -Justin
> 
>             Pooja
> 
> 
> 
> 
> 
> 
> 
>             On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul
>             <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>                Sai Pooja wrote:
> 
>                    Follow-up. It is easy to make it work. Just needed to
>             be more
>                    rigorous. Thank you.
> 
> 
>                It would be helpful if you describe what you mean.  This
>             error
>                message is new to me, and appears to reflect new
>             mechanics in the
>                upcoming Gromacs release.  If you describe what the
>             problem was, how
>                you resolved it, what your pdb2gmx command line was, and
>             anything
>                else that might be useful, that would likely help others
>             solve this
>                issue in the future.
> 
>                -Justin
> 
>                    On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja
>             <saipooja at gmail.com <mailto:saipooja at gmail.com>
>                    <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com>> <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com>
> 
>                    <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com>>>> wrote:
> 
>                       I used -ter option and selected "none" for both
>             terminal ends
>                    but I
>                       still get this error:
> 
>                       Fatal error:
>                       There is a dangling bond at at least one of the
>             terminal ends.
>                       Select a proper terminal entry.
>                       For more information and tips for troubleshooting,
>             please
>                    check the
>                       GROMACS
>                        I have used Mark's definitions for capping
>             residues in the
>                    rtp file.
> 
>                       In the pdb file, this is what the capping residues
>             look like:
> 
>                       ATOM     33  N   CBX     5       8.609   2.722
>              18.430  1.00
>                     1.60         FR1
>                       ATOM     34  H   CBX     5       9.198   3.338
>              17.946  1.00
>                     0.80         FR1
>                       ATOM     35 CH3  CBX     5       7.176   2.594
>              17.895  1.00
>                     2.17         FR1
> 
>                       ATOM      1  CH3 ACE     1      12.782  -0.027
>              28.022  1.00
>                     2.17         FR1
>                       ATOM      2  C   ACE     1      12.532  -0.094
>              26.546  1.00
>                     2.10         FR1
>                       ATOM      3  O   ACE     1      13.443  -0.213
>              25.696  1.00
>                     1.60         FR1
> 
> 
> 
> 
> 
> 
>                       On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul
>                    <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
> 
> 
> 
>                           Sai Pooja wrote:
> 
>                               Thanks Marks. I tried it but this is what
>             I get:
> 
>                               Fatal error:
>                               atom N not found in buiding block 1ACE while
>                    combining tdb
>                               and rtp
>                               For more information and tips for
>             troubleshooting, please
>                               check the GROMACS
>                               website at
>             http://www.gromacs.org/Documentation/Errors
> 
>                               Do I need to edit the aminoacids.n.tdb
>             file as well?
> 
> 
>                           What are you choosing as your termini when running
>                    pdb2gmx?  It
>                           should be "none," since by capping, you are
>             not choosing a
>                           protonation state for the N- and C-termini.
> 
>                           -Justin
> 
> 
>                               Pooja
> 
> 
> 
>                               On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
>                               <mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>
>                    <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>
>             <mailto:mark.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
>                    <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>>
>                               <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>
>                    <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>
>                               <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>
>                    <mailto:mark.abraham at anu.edu.au
>             <mailto:mark.abraham at anu.edu.au>>>>> wrote:
> 
> 
> 
>                                  ----- Original Message -----
>                                  From: Sai Pooja <saipooja at gmail.com
>             <mailto:saipooja at gmail.com>
>                    <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
>                               <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com>
>                    <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com>>> <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com>
>                    <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
>                               <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
>             <mailto:saipooja at gmail.com>>>>>
>                                  Date: Friday, July 2, 2010 7:28
>                                  Subject: Re: [gmx-users] Capping residues
>                                  To: jalemkul at vt.edu
>             <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>             <mailto:jalemkul at vt.edu>>
>                    <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                               <mailto:jalemkul at vt.edu
>             <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>             <mailto:jalemkul at vt.edu>>
>                    <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>             <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>,
>                               Discussion list for
>                                  GROMACS users <gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>
>                    <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>>
>                               <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>
>                    <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>>>
>             <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> 
>                    <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>>
> 
>                               <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>
>                    <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>>>>>
> 
>                                   > I am sorry if I did not frame the
>             question
>                    correctly,
>                               but putting
>                                  it very simply, is there a way to use
>             capping residues
>                               with the
>                                  charmm forcefield if the residues are
>             --COCH3 and
>                    NHCH3?
> 
>                                  Yes - you edit a copy of the .rtp file
>             in your working
>                               directory and
>                                  add whatever you want. Here's what I
>             use in CHARMM
> 
>                                  [ ACE ]
>                                   [ atoms ]
>                                          CH3     CT3     -0.270  0
>                                          HH31    HA      0.090   0
>                                          HH32    HA      0.090   0
>                                          HH33    HA      0.090   0
>                                          C       C       0.510   1
>                                          O       O       -0.510  1
>                                   [ bonds ]
>                                          C       CH3
>                                          C       +N
>                                          CH3     HH31
>                                          CH3     HH32
>                                          CH3     HH33
>                                          O       C
>                                   [ impropers ]
>                                          C       CH3     +N      O
> 
>                                  [ NAC ]
>                                   [ atoms ]
>                                         N       NH1     -0.470  1
>                                         HN      H       0.310   1
>                                         CH3     CT3     -0.110  1
>                                         HH31    HA      0.090   1
>                                         HH32    HA      0.090   1
>                                         HH33    HA      0.090   1
>                                   [ bonds ]
>                                         -C      N
>                                         N       HN
>                                         N       CH3
>                                         CH3     HH31
>                                         CH3     HH32
>                                         CH3     HH33
> 
>                                   [ impropers ]
>                                         N       -C      CH3     HN
>                                         -C      CH3     N       -O
> 
>                                  Mark
>                                  --
>                                  gmx-users mailing list  
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> 
> 
>                               --             Quaerendo Invenietis-Seek
>             and you
>                    shall discover.
> 
> 
>                           --        
>             ========================================
> 
>                           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>
>             <http://vt.edu> <http://vt.edu> |
> 
>                    (540) 231-9080
> 
>                          
>             http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
>                       --     Quaerendo Invenietis-Seek and you shall
>             discover.
> 
> 
> 
> 
>                    --         Quaerendo Invenietis-Seek and you shall
>             discover.
> 
> 
>                --     ========================================
> 
>                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> <http://vt.edu> |
>             (540) 231-9080
>                http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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>             -- 
>             Quaerendo Invenietis-Seek and you shall discover.
> 
> 
>         -- 
>         ========================================
> 
>         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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> 
> 
>     -- 
>     Quaerendo Invenietis-Seek and you shall discover.
> 
> 
> 
> 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.

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

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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