[gmx-users] 회신: Re: Generating topology file containing HYP

[Ming Tang]

Hi, Sangeun

Thank you so much for your detailed instruction. I can mutate PRO to HYP now.
Regards,

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of sangeunjee
Sent: Friday, 1 May 2015 9:36 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] 회신: Re: Generating topology file containing HYP

Dear Ming Tang

I am also using free version. To concert proline to hydroxypropine, 1. Read your pdb file using discovery studio visualizer 2. You will find there is list of menu in the left side of the screen. There is an option to draw specific amino acids. Here you can choose mutate to change proline to other one. I hope it helps,

Sangeun Jee

<div>-------- 원본 메시지 --------</div><div>발신: Ming Tang <m21.tang at qut.edu.au> </div><div>날짜:30/04/2015  02:09  (GMT-05:00) </div><div>수신: gmx-users at gromacs.org </div><div>제목: Re: [gmx-users] Generating topology file containing HYP </div><div> </div>Dear, sangeun

Thanks for your help. I have downloaded and installed Discovery Studio Visualizer, and found only limited amount of its ability is available for free. Do you think I can convert proline into hydroxyproline using its free function?
Detail guidance will be appreciate.

Thanks in advance,
Best regards. 

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of sang eun jee
Sent: Thursday, 30 April 2015 1:01 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Generating topology file containing HYP

Dear Ming Tang

As long as I know, Discovery studio visualizer can do the mutation from proline to hydroxyproline in a simple way.

Hope it helps,

Sangeun Jee

On Wed, Apr 29, 2015 at 5:42 AM, Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear all,
>
> I have a pdb file, and need to convert some of the proline to 
> hydroxyproline. Can I use pdb2gmx to convert proline to hydroxyproline 
> when generating the topology file?  If I cannot, then which kind of 
> software can be used to convert proline to hydroxyproline when 
> generating the topology file?
>
> Thanks in advance,
> Regards,
> Ming
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