Re: [gmx-users] Capping residues

[Justin A. Lemkul]

Sai Pooja wrote:
Hi Justin,

I do not have the problem of extra hydrogens or a net charge on the NAC 
group. 


The net charge is not on NAC, it's on the entire peptide.  If you're not seeing 
it, that makes the bug even more troubling, since it's sporadic.  Are you using 
the latest git version, or an older one?  If it's older, that may help track 
down the code change that is causing problems.

In relation to the other bugs you have mentioned, would it be a good 
idea to start a project with this git version of gromacs? The topology 
file I have now looks fine but I may be missing certain irregularities. 
Is there a good way to check?


I would never recommend using a git version for production work.  It is under 
continual development (thanks to the hard work of the developers!) and as such, 
small (or large) bugs may get occasionally introduced, or new features added or 
modified.  I would only suggest using a git version for actual data collection 
if it fixes a specific bug that was a problem for you and the git version fixes 
it and is stable.

As far as checking, I have no idea.  The test suite needs to be developed 
further before there is a useful set of tools for validating a GROMACS installation.

Is there another safe way to use the charmm forcefield with 
gromacs(without gromacs)?


Supposedly the CHARMM implementation in GROMACS is stable, but maybe changes in 
the code have given rise to the bugs I'm suspecting.  I can't even get a 
topology for lysozyme; there are a host of errors which are concerning to me.

Otherwise use the CHARMM program, or even NAMD.

-Justin

Pooja


On Wed, Jul 7, 2010 at 8:48 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    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 <saipo...@gmail.com
        <mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com
        <mailto:saipo...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
           <mailto:jalem...@vt.edu <mailto:jalem...@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
                   <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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
                   <saipo...@gmail.com <mailto:saipo...@gmail.com>
        <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>
                          <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>
                   <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>>> <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>

                   <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>

                          <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>
                   <mailto:saipo...@gmail.com
        <mailto:saipo...@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
                          <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
                             <mailto:jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@vt.edu>>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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.abra...@anu.edu.au
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                   <mailto:mark.abra...@anu.edu.au
        <mailto:mark.abra...@anu.edu.au>>>>>> wrote:



                                        ----- Original Message -----
                                        From: Sai Pooja
        <saipo...@gmail.com <mailto:saipo...@gmail.com>
                   <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>
                          <mailto:saipo...@gmail.com
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        <mailto:saipo...@gmail.com>>>
                                     <mailto:saipo...@gmail.com
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                   <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>
                          <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>
                   <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>>>> <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>
                   <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>
                          <mailto:saipo...@gmail.com
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        <mailto:saipo...@gmail.com>
                   <mailto:saipo...@gmail.com
        <mailto:saipo...@gmail.com>>>>>>
                                        Date: Friday, July 2, 2010 7:28
                                        Subject: Re: [gmx-users] Capping
        residues
                                        To: jalem...@vt.edu
        <mailto:jalem...@vt.edu>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
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                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>
                                     <mailto:jalem...@vt.edu
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                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
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                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
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                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>>,
                                     Discussion list for
                                        GROMACS users
        <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
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        <mailto:gmx-users@gromacs.org>>>>
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                          <mailto:gmx-users@gromacs.org
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                   <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>>>

                                     <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>
                   <mailto:gmx-users@gromacs.org
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                                         > 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
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