[gmx-users] top/itp file to show parameters explicitly

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 23 10:47:05 CEST 2012


On 23/05/2012 6:42 PM, Alan wrote:
> Thanks Justin, you were right. In the end gmxdump helped to clear some 
> doubts but I wished it would be less painfully.

One useful approach is to simplify the system as much as possible before 
producing the .tpr and using gmxdump. The necessary cross-referencing is 
easier to see when the complexity of the contents is low.

Mark

>
> Cheers,
>
> Alan
>
> On 22 May 2012 12:36, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 5/22/12 12:46 PM, Alan wrote:
>
>         Hi Justin, your suggestion got close. However, let me give an
>         example. You can
>         use the Gly-Gly-Gly example I am attaching and do this:
>
>         pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top
>          -water none
>         /sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr
>         -pp aGGGp.top
>
>         if you look at aGGGp.top I can't find which parameters were
>         used for
>
>         [ dihedrals ]
>         ;  ai    aj    ak    al funct            c0            c1    
>                c2
>            c3            c4            c5
>             2     1     5     6     9
>
>         I.e., for proper dihedral (H1-     N-    CA-   HA1), I can't find
>         in amber99sb.ff/forcefield.itp any combination that handles
>         parameters for
>         X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral?
>
>
>     Make sure you're looking at types, not names.  The type sequence
>     here is H-N3-CT-HP, which I think is mapped to this dihedral:
>
>      X   CT  N3  X     9       0.0      0.65084     3  ; JCC,7,(1986),230
>
>     Running gmxdump on the .tpr file will show it for sure; I had
>     assumed it would be in the post-processed topology as well, but I
>     guess not.
>
>     -Justin
>
>         Thanks,
>
>         Alan
>
>         On 21 May 2012 18:50, Justin A. Lemkul <jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
>            On 5/21/12 2:43 PM, Alan wrote:
>
>                Hi there,
>
>                Is there an option in pdb2gmx that when generating the
>         top/itp file, it
>                could
>                show the parameters explicitly? e.g.:
>
>                Instead of:
>                [ dihedrals ]
>                ;  ai    aj    ak    al funct            c0          
>          c1            c2
>                    c3
>                     5    13    11    12     4
>                    11    15    13    14     4
>                    15    23    21    22     4
>                    21    25    23    24     4
>                    25    32    31    33     4
>
>                (my hard hand modifications)
>
>                [ dihedrals ] ; impropers
>                ; treated as propers in GROMACS to use correct AMBER
>         analytical function
>                ;    i      j      k      l   func   phase     kd      pn
>                      5     13     11     12      4   180.00  43.93200
>           2 ;     CA-     N-
>                C-     O
>                     11     15     13     14      4   180.00   4.60240
>           2 ;      C-    CA-
>                N-     H
>                     15     23     21     22      4   180.00  43.93200
>           2 ;     CA-     N-
>                C-     O
>                     21     25     23     24      4   180.00   4.60240
>           2 ;      C-    CA-
>                N-     H
>                     25     32     31     33      4   180.00  43.93200
>           2 ;     CA-   OC1-
>                C-   OC2
>
>                I mean, if the parameters that are hiding in e.g.
>                ...gromacs/top/amber99sb.ff
>                could be showed in the top/itp file for human readers,
>         that would be great.
>
>
>            You can obtain these parameters (I believe) by running
>         grompp with the -pp
>            option.  If you think it would be a useful feature for
>         pdb2gmx, file a
>            feature request on redmine.gromacs.org
>         <http://redmine.gromacs.org> <http://redmine.gromacs.org>.
>
>            -Justin
>
>            --
>            ==============================__==========
>
>
>            Justin A. Lemkul, Ph.D.
>            Research Scientist
>            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
>         <http://vt.edu/Pages/Personal/justin>
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
>            ==============================__==========
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>         --
>         Alan Wilter SOUSA da SILVA, DSc
>         Bioinformatician, UniProt - PANDA, EMBL-EBI
>         CB10 1SD, Hinxton, Cambridge, UK
>         +44 1223 49 4588 <tel:%2B44%201223%2049%204588>
>
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul, Ph.D.
>     Research Scientist
>     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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> -- 
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
>
>
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