[gmx-users] pdb2gmx changes conformation?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jan 24 19:53:36 CET 2012

Hi Igor,

Please look at the contents of the files. Note the order of atoms.



On Jan 24, 2012 7:31 PM, "" <shch406 at bpci.kiev.ua> wrote:


I applied *pdb2gmx* to PDB file *A.pdb* with force field *gromos53a5*  and
water model *spc* and then compared the resulting *A.gro* file with initial
PDB one, using program *g_rmsdist* by the following command:

* /opt/software/gromacs/gromacs-4.5.3-intel/bin/g_rmsdist -f A.gro -s
/home/shch406/PDB/A.pdb -o A.dA.xvg *
Structures appeared to be quite different - RMSD = 1.67!

*@ subtitle "of distances between Protein atoms"*

*0 1.67265*

Thanks in advance,

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