[gmx-users] topology can't be generated by pdb2gmx with drude force field embedded

严攀 1281465591 at qq.com
Tue Dec 10 03:32:01 CET 2019


Hello everyone   There's a problem that's been bothering me for a long time, I've embedded the drude polarizable in gromacs via cloning the soure code from github. when I tried to generate topology via pdb2gmx, the terminal always prompts me for such an error: "Fatal error: Residue 'HOH' not found in residue topology database". Actually, I used the swm1024.gro file from the charmm's websitehttp://mackerell.umaryland.edu/charmm_drude_ff.shtml, so I think there's little possibility of error in the gro file. I chose the SWM4_NDP water when prompted a choice. So how can I fix this problem? Beat RegardsTina


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