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

[Justin Lemkul]

On 12/9/19 9:51 PM, 严攀 wrote:
> Hello everyone   There's a problem that's been bothering me for a long time， I've embedded the drude polarizable force field 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?  Or where is this supported to go wrong? I'm not sure whether the problem is with the drude force filed files or my operations? Have anyone else ever met this probelm?  Beat RegardsTina
The file provided at 
http://mackerell.umaryland.edu/charmm_drude_ff.shtml uses "SOL," not 
"HOH" so I do not know why your file as HOH in it.

-Justin

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Justin A. Lemkul, Ph.D.
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