[gmx-users] HB3 ATOM

[Justin Lemkul]

On 9/3/18 2:28 PM, Mahdi Sobati Nezhad wrote:
> how can I build hydrogens own, after -ignh command?!

Please re-read what I just said.

-Justin

> On Mon, 3 Sep 2018 22:55 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> On 9/3/18 2:24 PM, Mahdi Sobati Nezhad wrote:
>>> Yes. Now my problem is HG in residue CYS that I don't know rename to
>> what!!!
>>
>> Either the names in the PDB file need to be made consistent with what is
>> in the .rtp file, or you should use -ignh to have pdb2gmx ignore all
>> input H atoms and build its own, all of which will be properly named.
>>
>> -Justin
>>
>>> On Mon, 3 Sep 2018 22:49 Justin Lemkul, <jalemkul at vt.edu> wrote:
>>>
>>>> On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote:
>>>>> Hi
>>>>> my pdb file named HB2 and HB3 but .rtp file in  my force field named
>>>> HB1and
>>>>> HB2. and so on error "atom HB3 in residue xxx was not found in rtp
>> entry"
>>>>> can I rename HB2 to HB1 and HB3 to HB2 ?
>>>>> or any idea?!
>>>> Have you tried it?
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 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
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

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