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

[Justin Lemkul]

On 12/30/19 5:35 AM, 严攀 wrote:
> Thanks for your answer, though I still can't solve this problem. I guess maybe there is some bug in the development of drude poparizable field.
>

You have provided no evidence of a bug. The original problem was the use 
of an invalid residue name, and without further information, there's 
nothing anyone can do to help, but it's very presumptuous to say that 
anything is buggy, particularly the force field (which I have validated 
quite extensively).

-Justin

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>
> ------------------ 原始邮件 ------------------
> 发件人:&nbsp;"严攀"<1281465591 at qq.com&gt;;
> 发送时间:&nbsp;2019年12月10日(星期二) 上午10:51
> 收件人:&nbsp;"gmx-users"<gmx-users at gromacs.org&gt;;
>
> 主题:&nbsp;topology can't be generated by pdb2gmx with drude force field embedded
>
>
>
> 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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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