On 2/3/18 1:39 PM, Seera Suryanarayana wrote:
Dear gromacs users
I done simulations of peptide of 20 residues length for 300ns. As I would
like to explore the conformational flexibility I have chosen to do dPCA. I
have gone through the tutorial which is present in the gromacs cite.
Firstly, I have created the index file which shows the dihedral angle atom
numbers. I have given the 36 dihedral angles information of 18 residues.
Based on the formula 2*N/3 for 24 atoms I can create index file which can
be used in the neat step to create the .gro file. In my index file I gave
first 24 backbone atoms numbers. When use the gmx trjconv for getting
resized.gro I got following error.
Fatal error:
Index[4] 25 is larger than the number of atoms in the
trajectory file (24). There is a mismatch in the contents
of your -f, -s and/or -n files.
I got error meaning. In my index file fifth element is 25 which is greater
than the total number of atoms number that is 24. If I give first 24
numbers Then I got .gro file only for first file as follow.
Generated by trjconv : Protein in water t= 0.00000
24
1LYS N 1 -0.370 -0.929 0.912
1LYS H1 2 0.411 0.167 -0.986
1LYS H2 3 -0.533 0.846 -0.352
1LYS H3 4 -0.936 -0.603 0.798
1LYS CA 5 0.049 -0.999 -1.000
1LYS HA 6 -0.003 0.264 -0.965
1LYS CB 7 0.935 -0.356 0.188
1LYS HB1 8 -0.982 0.862 -0.506
1LYS HB2 9 0.358 -0.934 0.839
1LYS CG 10 -0.544 0.010 -1.000
1LYS HG1 11 -0.646 0.763 -0.335
1LYS HG2 12 -0.942 -0.930 -0.367
1LYS CD 13 0.374 -0.927 -0.662
1LYS HD1 14 0.750 0.341 -0.940
1LYS HD2 15 -0.661 0.751 -0.775
1LYS CE 16 -0.632 -0.591 0.807
1LYS HE1 17 -0.561 0.828 0.693
1LYS HE2 18 0.721 0.610 -0.793
1LYS NZ 19 -0.410 0.912 -0.585
1LYS HZ1 20 -0.811 -0.419 0.908
1LYS HZ2 21 0.054 -0.999 -0.159
1LYS HZ3 22 0.987 0.203 -0.979
1LYS C 23 0.749 -0.663 -0.820
1LYS O 24 -0.573 -0.900 0.436
2.00000 2.00000 2.00000
But I want to get the information for first 10 residues of my peptide.
Kindly tell me how to do get dPCA for first ten residues of my 20 residues
simulated peptide.
It seems you only saved the first residue in your trajectory. If you
make matching trajectory and .tpr files that save the first ten
residues, then you should be able to proceed.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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