Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + RTP (Remdesivir Tri-Phosphate) model, All Atom model (100 ns)
OpenVaibhav Modi;
MD-A001RE
Vaibhav Modi;
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-RTP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
LQSADAQSFL NRVCGVSAAR LTPCGTGTST DVVYRAFDIY NDKVAGFAKF LKTNCCRFQE KDEDDNLIDS YFVVKRHTFS NYQHEETIYN LLKDCPAVAK HDFFKFRIDG DMVPHISRQR LTKYTMADLV YALRHFDEGN CDTLKEILVT YNCCDDDYFN KKDWYDFVEN PDILRVYANL GERVRQALLK TVQFCDAMRN AGIVGVLTLD NQDLNGNWYD FGDFIQTTPG SGVPVVDSYY SLLMPILTLT RALTAESHVD TDLTKPYIKW DLLKYDFTEE RLKLFDRYFK YWDQTYHPNC VNXLDDRXIL HXANFNVLFS TVFPPTSFGP LVRKIFVDGV PFVVSTGYHF RELGVVHNQD VNLHSSRLSF KELLVYAADP AMHAASGNLL LDKRTTCFSV AALTNNVAFQ TVKPGNFNKD FYDFAVSKGF FKEGSSVELK HFFFAQDGNA AISDYDYYRY NLPTMCDIRQ LLFVVEVVDK YFDCYDGGXI NANQVIVNNL DKSAGFPFNK WGKARLYYDS MSYEDQDALF AYTKRNVIPT ITQMNLKYAI SAKNRARTVA GVSICSTMTN RQFHQKLLKS IAATRGATVV IGTSKFYGGW HNMLKTVYSD VENPHLMGWD YPKCDRAMPN MLRIMASLVL ARKHTTXXSL SHRFYRLANE CAQVLSEMVM CGGSLYVKPG GTSSGDATTA YANSVFNICQ AVTANVNALL STDGNKIADK YVRNLQHRLY ECLYRNRDVD TDFVNEFYAY LRKHFSMMIL SDDAVVCFNS TYASQGLVAS IKNFKSVLYY QNNVFMSEAK CWTETDLTKG PHEFCSQHTM LVKQGDDYVY LPYPDPSRIL GAGCFVDDIV KTDGTLMIER FVSLAIDAYP LTKHPNQEYA DVFHLYLQYI RKLHDELTGH MLDMYSVMLT NDNTSRYWEP EFYEAMYTPH TVL
EDKRAKVTSA MQTMLFTMLR KLDNDALNNI INNARDGCVP LNIIPLTTAA KLMVVIPDYN TYKNTCDGTT FTYASALWEI QQVVDADSKI VQLSEISMDN SPNLAWPLIV TALRANSAVK LQ
SKMSDVKCTS VVLLSVLQQL RVESSSKLWA QCVQLHNDIL LAKDTTEAFE KMVSLLSVLL SMQGAVDINK LCEEMLDNRA TLQ
CCAGUUCUCU CGUCCGGA
GCCCGGACGA GAGA
| Run | Outputs |
|---|---|
| replica 1 | TrajectoryAnalyses |
48 files · 340 MB
