[gmx-users] Regarding DPCA
matthias.ernst at physik.uni-freiburg.de
Mon Feb 5 11:53:42 CET 2018
Sorry to pop in without actually addressing your questions.
But, as the question for dPCA comes up every year or so, let me just
state what I wrote some time ago:
In my opinion, the way dPCA is described on the GROMACS page is rather
misleading and prone to errors. Don't do it that way.
Better use some tool of your choice to write out the dihedral angles as
ASCII file (it's much easier to see if everything worked out in this
case anyway) and use FastPCA (https://github.com/lettis/FastPCA) for
actually performing the PCA. All data (covariance matrix, eigenvectors
and -values and principal components) then are generated as ASCII files
as well and can be analysed and plotted with the tool of your choice.
In addition, please note that it is possible to perform dPCA without
doing the sine/cosine transformation, see
https://doi.org/10.1063/1.4998259. We recommend using this procedure as
in this case, the covariance matrix and eigenvectors can readily be
interpreted (e.g., dihedral x is the moste important one...)
Am 05.02.2018 um 10:17 schrieb Seera Suryanarayana:
>> 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 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
>> 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.
> Dear Justin
> In brief I would like to tell you my problem. I have taken the atom numbers
> those represent the dihedral angle atoms from the topology file to generate
> the index file to generate .trr file. Then I have generated the another
> index file for .gro file. As number of dihedral angles 36 for 18 residues,
> I could save 24 atoms according to 2*N/3 formula. As my area of interest is
> first 2-12 residues, I have taken numbers of backbone atoms in my index
> file for resized.gro file. Then I executed the following command
> trjconv -s foo.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0
> Here I got the error as follow
>> Fatal error:
>> Index 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.
> Now come to your suggestion, you suggested me that first make matching
> trajectory and .tpr files for 10 residues. Here I not able to getting how
> does that work. Because we have to generate the .trr file based on the
> dihedral index file, which means definitely I will get the same error.
> Kindly tell me more about how to generate the resized.gro file for first 10
> Thanks in advance
> Graduate student
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