[gmx-users] Problems with g_anaeig!

[Florian Haberl]

hi,

On Tuesday 18 July 2006 12:12, Semen Esilevsky wrote:
> Dear gmx users,
> I've found a strange problem in g_anaeig.
> I'm trying to project the trajectory into few first
> eigenvectors. For this I first do:
>
> g_covar -f md_all.xtc -s md0.tpr -n index.ndx -fit
> -ref -pbc -tu ns
>
> Chosing CA group for matrix construction.
> Then I pick the resulting file eigenvec.trr and do:
>
> g_anaeig -v eigenvec.trr -f md_all.xtc -s md0.tpr
> -filt -n index.ndx -first 1 -last 10
>
> Everything works fine and the output file filtered.xtc
> should contain nice filtered trajectory. Ok, let's
> test:
>
> g_covar -f filtered.xtc -s md0.tpr -n index.ndx -fit
> -ref -pbc -tu ns
> ...
> ...
> ...
> Calculating the average structure ...
> Reading frame       0 time    0.000
> -------------------------------------------------------
> Program g_covar, VERSION 3.3.1
> Source code file: mshift.c, line: 118
>
> Fatal error:
> Molecule in topology has atom numbers below and above
> natoms (238).
> You are probably trying to use a trajectory which does
> not match the first 238 atoms of the run input file.
> You can make a matching run input file with tpbconv.
> -------------------------------------------------------
>
> What is wrong? It should be the same trajectory as
> initial md_all.xtc but with different numbers.
> Any ideas?

You have to use also a reference file with the same amount of atoms in it, 
like your new trajectory.

Use something like trjconv or as the error msg say tpbconv to write out a 
gro/pdb file only with CA atoms.

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Greetings,

Florian
-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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