[gmx-users] How to create top of small molecules with pdb2gmx

[Tingguang.S]

Thank you Justin,


I had tried many times, and the interactive selection still didn't work, I really need help. I downloaded charmm36-nov2018.ff.tgz from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs,  and extracted it into /usr/local/gromacs/share/gromacs/top. 


I had attached the log file, and pdb file of formic acid. Please help with this.


Thank you for your time!




发件人：Justin Lemkul <jalemkul at vt.edu>
发送日期：2019-03-28 21:48:32
收件人：gmx-users at gromacs.org
主题：Re: [gmx-users] How to create top of small molecules with pdb2gmx>
>
>On 3/28/19 9:36 AM, Tingguang.S wrote:
>> Thank you, Justin！
>>
>>
>> You mean that I should use the following command:  "gmx pdb2gmx -f formic-acid.pdb -ter "？
>> I had used the flag -ter, but the program did not prompt interactive selection.
>
>I don't know how that could have happened. The purpose of -ter is to 
>trigger an interactive selection.
>
>-Justin
>
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>Justin A. Lemkul, Ph.D.
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