[gmx-users] Recentering a protein

Ahmed Mashaly mashaly_1988 at yahoo.com
Thu Jan 18 17:14:13 CET 2018

I am new to gromacs (using v. 2016.4) and need to check the following steps for my system.
01. I have prepared the system with Amber 14, minimized, heated to 300K, equilibrated 02. Then I used Acpype to convert the amber top and equilibrated rst file to gromacs .top and .gro files03. Changing Na+ to NA and WAT to SOL and H and O of water to HW1 HW2 and OW04. Doing a CG minimization again with gromacs.05. Doing a NPT with gromacs06. Running MD simulation with gromacs.
Is this procedure correct or do I need any modification?
In Amber we used to run MD for 5 ns, then recenter then relaunch from the last rst file. The same case will be with gromacs.Is there a script I can find to recenter and relunch the process automatically?

Another thing after doing the minimization, I cannot recenter the protein by trjconv command gmx trjconv -f em.gro -s em.tpr -o em_1.gro -center -pbc mol -ur compact>> selecting 1 to center protein>> selecting 0 to get the whole system output
In this link you have The acp.gro and acp.top file produced from Acpype with modifications to Na and watermdp files for Min, NPT, MD, please check themAnd the em.gro the file produced after minimization which cannot be centered
Many thanks
Kind Regards,Ahmed 

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