[gmx-users] SDF-error

[delara aghaie]

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???

Thanks for  your time
Regards
D.M







and then
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