[gmx-users] SDF-error

[Justin A. Lemkul]

On 6/17/12 8:35 AM, delara aghaie wrote:
> Dear Gromacs users
> I want to calculate SDF for water molecules around protein.
>
> I use these command line:
> trjconv -s ../md_0_1.tpr -f ../md_0_1.xtc -o first.xtc -boxcenter tric -ur
> compact -pbc none
> This asks me to
> Select group for output
> Group     0 (         System) has 41559 elements
> Group     1 (        Protein) has  2698 elements
> Group     2 (      Protein-H) has  1351 elements
> Group     3 (        C-alpha) has   165 elements
> Group     4 (       Backbone) has   495 elements
> Group     5 (      MainChain) has   661 elements
> Group     6 (   MainChain+Cb) has   821 elements
> Group     7 (    MainChain+H) has   823 elements
> Group     8 (      SideChain) has  1875 elements
> Group     9 (    SideChain-H) has   690 elements
> Group    10 (    Prot-Masses) has  2698 elements
> Group    11 (    non-Protein) has 38861 elements
> Group    12 (          Water) has 38859 elements
> Group    13 (            SOL) has 38859 elements
> Group    14 (      non-Water) has  2700 elements
> Group    15 (            Ion) has     2 elements
> Group    16 (            NA+) has     2 elements
> Group    17 ( Water_and_ions) has 38861 elements
>
> Here I select group (13)
>
> Then this command line:
> trjconv -s ../md_0_1.tpr -f first.xtc -o second.xtc -fit rot+trans
> It asks for two groups:
>
> Select group for least squares fit
> Group     0 (         System) has 41559 elements
> Group     1 (        Protein) has  2698 elements
> Group     2 (      Protein-H) has  1351 elements
> Group     3 (        C-alpha) has   165 elements
> Group     4 (       Backbone) has   495 elements
> Group     5 (      MainChain) has   661 elements
> Group     6 (   MainChain+Cb) has   821 elements
> Group     7 (    MainChain+H) has   823 elements
> Group     8 (      SideChain) has  1875 elements
> Group     9 (    SideChain-H) has   690 elements
> Group    10 (    Prot-Masses) has  2698 elements
> Group    11 (    non-Protein) has 38861 elements
> Group    12 (          Water) has 38859 elements
> Group    13 (            SOL) has 38859 elements
> Group    14 (      non-Water) has  2700 elements
> Group    15 (            Ion) has     2 elements
> Group    16 (            NA+) has     2 elements
> Group    17 ( Water_and_ions) has 38861 elements
>
> Here I choose group (4) protein backbone
> ------ and then
> Selected 4: 'Backbone'
> Select group for output
> Group     0 (         System) has 41559 elements
> Group     1 (        Protein) has  2698 elements
> Group     2 (      Protein-H) has  1351 elements
> Group     3 (        C-alpha) has   165 elements
> Group     4 (       Backbone) has   495 elements
> Group     5 (      MainChain) has   661 elements
> Group     6 (   MainChain+Cb) has   821 elements
> Group     7 (    MainChain+H) has   823 elements
> Group     8 (      SideChain) has  1875 elements
> Group     9 (    SideChain-H) has   690 elements
> Group    10 (    Prot-Masses) has  2698 elements
> Group    11 (    non-Protein) has 38861 elements
> Group    12 (          Water) has 38859 elements
> Group    13 (            SOL) has 38859 elements
> Group    14 (      non-Water) has  2700 elements
> Group    15 (            Ion) has     2 elements
> Group    16 (            NA+) has     2 elements
> Group    17 ( Water_and_ions) has 38861 elements
> Select a group:
>
> again I select 13 for SOL
> ======================================Below is the error which I
> get:::::::::::::::::::
>
> Back Off! I just backed up second.xtc to ./#second.xtc.5#
>
> -------------------------------------------------------
> Program trjconv, VERSION 4.5.5
> Source code file: gmx_trjconv.c, line: 1166
>
> Fatal error:
> Index[36161] 38860 is larger than the number of atoms in the
> trajectory file (38859). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> =================================================================
> I have checked my .gro file from which md_0_1.tpr has created. It has 41559 atoms
> also in topology file I have one protein with 2698 atoms, 12953 water molecules
> (==38859 atoms) and 2 ions which gives in total 41559 atoms.
> =========================================
> ************I do not undestand the error.
> **********Also please let me know if I want to calculate water SDF around
> protein backbone, are my group selections fine???
>

Your selections create a fragmented trajectory that trjconv cannot deal with. 
In your first command, you output only solvent.  Then, you try to use a 
solvent-only trajectory to do fitting to a protein backbone.  You should output 
the whole system in the first step.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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