normal Backmapping - problem with the output structure

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1 month 3 weeks ago #7754 by z.sichaib
z.sichaib created the topic: Backmapping - problem with the output structure
Dears,

I'm using the following command to backmap a CG protein to AA:
./initram-v5.sh -f protein_CG.gro -o protein_aa.gro -to amber -p topol.top

The program runs without any issues but when I visualize the AA structure, this last is weird. It looks broken, fragmented into 8 different pieces (?). I don't know if it's a PBC problem or something else. You can see a picture of how the final aa system looks like here: www.dropbox.com/s/smncxffmfz7ztd9/backmap.png?dl=0


I would really appreciate any help/ advice, please.

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1 month 3 weeks ago #7755 by riccardo
riccardo replied the topic: Backmapping - problem with the output structure
Does the protein run after backmapping? If so, I guess that you don't have any real issue, it is just that your protein is at the "edge" of the coordinate system (e.g., centered at 0,0,0) and thus gets split in the visualization. Another way to check would be running:

gmx trjconv -f protein_which_looks_split.gro -o whole_protein.gro -pbc whole -s topol-AA.tpr

and try to visualize "whole_protein.gro".

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1 month 3 weeks ago #7756 by z.sichaib
z.sichaib replied the topic: Backmapping - problem with the output structure
Hi Riccardo,

It's working! Thank you so much!

Best,

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