[gmx-users] TPO and SEP is is added in residue.date
mehreen_jan1990 at yahoo.com
Mon May 9 06:46:34 CEST 2016
thank you for your response!
i run phosphorylated simulation 10ns result are good known i want to extend my simulation to 20ns the problem is at 11ns i generate PDB i am shocked to see that my TPO and SEP is no more in the pdb. structure is breakdown :( i have no idea what happen to my pdb :( :(
1) have added these residues to residuetypes.dat
i am saving "Protein" when selecting output from trjconv. because it it is protein domain
command to extend:
convert-tpr -s md_0_1.tpr -extend 1000 -o next1.tpr
mdrun -s next1.tpr -cpi md_0_1.cpt
to combine xtc command:
trjcat -f md_0_1.xtc next1.xtc next2.xtc -o concat.xtc -cat
to generate PDB:
trjconv -s md_0_1.tpr -f md_0_1.xtc -o time_11000ps.pdb -dump 11000
and when i open PDB TPO and SEP is disappear from PDB and structure is break down.
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