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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.