[gmx-users] Two polypeptides in one box

[Yang Ye]

Hi,

editconf -h

-rotate shall follow three numbers.

Regards,
Yang Ye

On 5/20/2007 8:12 AM, Sheyore Omovie wrote:
> Hi Yang,
> Thanks.
> But I got the following error message when I tried to rotate the 
> molecule using editconf:
> 'Expected a real argument for option -rotate'
> What's the correct syntax for rotate. This is what i did at the prompt:
> editconf -rotate sele.pdb
> Can u tell me what i'm doing wrong.
> Rgds
> John
>
>
>
>> From: Yang Ye <leafyoung at yahoo.com>
>> Reply-To: Yang Ye <leafyoung at yahoo.com>,Discussion list for GROMACS 
>> users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Two polypeptides in one box
>> Date: Sat, 19 May 2007 10:34:56 -0700 (PDT)
>>
>> To combine two structures, use editconf to translate/rotate each 
>> first and combine with a text editor.
>>
>> ----- Original Message ----
>> From: Sheyore Omovie <omovie_johnnie at hotmail.com>
>> To: gmx-users at gromacs.org
>> Sent: Sunday, May 20, 2007 1:22:15 AM
>> Subject: [gmx-users] Two polypeptides in one box
>>
>>
>> Hi gromacs users,
>> I want to simulate interaction between two polypeptides in one box. I 
>> have
>> read Tsjerk response to a similar question. However, i dont know just 
>> how to
>> implement it, i.e how do I position two pdb files using editconf and 
>> create
>> one pdb file. If possible I'll appreciate specific commands on how to
>> implement this.
>> I also tried using pymol, but because I'm also new to this software, 
>> I could
>> not figure it out.
>> Regards
>> John
>>
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