[gmx-users] TPO and SEP is is added in residue.date

[Mehreen Jan]

respected sir!
thank you for your response!

version 5.0.7
forcefield 43a1p
Question 1
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.