Date: Tue, 4 Jun 2019 11:00:27 +0100
Dear All,
I noticed that there are (small) differences in PDB file formats between
RCSB and AMBER.
Is it possible to convert MD trajectories snapshots back into RCSB format
since I find that other programs like LeVIew, which can be used for active
site interaction maps, don't read amber generated PDB files and require
RCSB formats? Is it going to be tricky for non-standard residues, I'm
guessing it shouldn't be since amber starts with the RCSB format?
Is it possible to generate 2D interaction images using AmberTools?
I think cpptraj or other ambertools can write in text files, that's good
for analyzing larger datasets/trajectories, but sometimes one prefers to
look at the 2D interaction maps like the following (to keep track of imp
residues etc).
thanks in advance.
LeView 2D interaction map
[image: image.png]
LeView interaction text output
******************Hydrogen bonds******************
donnor_atom residue acceptor_atom residue distance
NE2_638 GLN_286(A) O2_4418 BRL_1(A) 2.9125
OG_666 SER_289(A) O4_4419 BRL_1(A) 2.7697
NE2_934 HIS_323(A) O4_4419 BRL_1(A) 2.7718
N3_4421 BRL_1(A) OH_2140 TYR_473(A) 3.0411
*****************Nearby residues*****************
ligand_atom residue nearby_atom residue distance
C21_4440 BRL_1(A) CG2_598 ILE_281(A) 3.7176
O2_4418 BRL_1(A) CE1_608 PHE_282(A) 3.4511
C19_4438 BRL_1(A) C_622 GLY_284(A) 3.6509
C8_4429 BRL_1(A) O_627 CYS_285(A) 3.6201
C6_4427 BRL_1(A) OH_971 TYR_327(A) 3.6630
O13_4420 BRL_1(A) CD1_993 LEU_330(A) 3.7176
C16_4436 BRL_1(A) O_1061 LEU_340(A) 3.9564
N16_4422 BRL_1(A) CG2_1072 ILE_341(A) 3.3494
C21_4440 BRL_1(A) CE_1124 MET_348(A) 3.8267
C11_4432 BRL_1(A) SD_1261 MET_364(A) 3.4356
O2_4418 BRL_1(A) NE2_1942 HIS_449(A) 2.9740
O2_4418 BRL_1(A) CD1_1973 LEU_453(A) 3.7642
-- Regards, Dr. Vaibhav A. Dixit, Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. AND Assistant Professor, Department of Pharmacy, ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ Birla Institute of Technology and Sciences Pilani (BITS-Pilani), VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031. India. Phone No. +91 1596 255652, Mob. No. +91-7709129400, Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra P Please consider the environment before printing this e-mail
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