[gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

Ming Tang m21.tang at qut.edu.au
Fri May 1 02:35:16 CEST 2015

Thanks, Justin

It is a paper published in NANO-LETTERS!

-----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 Justin Lemkul
Sent: Friday, 1 May 2015 12:04 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

On 4/30/15 9:57 AM, Mark Abraham wrote:
> Hi,
> Please do everyone the courtesy of starting a new email, rather than 
> replying to a digest and confusing the archive and email readers.
> On Thu, Apr 30, 2015 at 3:50 PM Ming Tang <m21.tang at qut.edu.au> wrote:
>> Hi,Justin
>> I have been told by an author of one journsl that pdb2gmx can convert 
>> PRO to HYP while generating. I did not find the option. Can you give 
>> me some advice.
> Get knowledgeable reviewers ;-) You can't do it with pdb2gmx. Some 
> building programs are suggested on the GROMACS website.

Perhaps one can play some tricks, but I agree with Mark.  Simply saying that pdb2gmx can do this is not true, at least not in a straightforward way.

The trick I might think of (caveat: untested!) is as follows:

1. Process the chain with normal PRO and build normal H on to the ring 2. Take that output and rename PRO->HYP, define .rtp and .hdb entries for HYP (or use whatever is already in the force field), rename the corresponding H atom to whatever the appropriate oxygen name is, and then re-process with pdb2gmx to build on the hydroxyl H atom 3. Minimize thoroughly

The above steps assume, of course, the use of an all-atom force field to get H built onto the ring.

This is a *very* crude approach and could distort geometry, so tread carefully. 
  The best approach is, as Mark says, use some molecule-editing software and build the structure appropriately.  My hack might work, but it's not the best way to do this.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

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