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

[Justin Lemkul]

On 3/28/19 9:03 PM, Tingguang.S wrote:
> 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.

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-Justin

>
> 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
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
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-- 
==================================================

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

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================