Hey Guys,
I am calculationg radius of gyration for 1ubq.
My reference file is a pdb file. and I cannot change it. So I have to deal with it!!
The problem is that I receive 2 warnings:
WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. and WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary.
This is my command:
gmx gyrate -s 1ubq.pdb -f 00001run.xtc -xvg none -o 00001_rg_system.xvg
What do you suggest?
Thank you!!
Maryam
Hi,
Warnings you received look harmless, unless you molecule flow around through pbc. I would center the molecule in the box first. trjconv it with '-pbc whole -center' flags:
gmx trjconv -pbc whole -center
-Alexandr
Before any calculation, you should unwrap the segments of the system.
Hi Ramin,
I got this from here:
trjconv_mpi -f all.xtc -s polyeqm.gro -o allnojump.xtc -pbc nojump >
http://thread.gmane.org/gmane.science.biology.gromacs.user/62268
Is this what you mean?
I am making sure that I have understood your point well; do you mean I must use: -pbc nojump?
Thanks,
Maryam
Maryam, why did not you try doing it in VMD, explained before?
Hi Ramin,
I did that!
The problem is that I have around 10,000 files! I don't wanna spend that much time.
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