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

[Mark Abraham]

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.

Mark


> Thanks
> Sent from my Huawei Mobile
>
> Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 4/30/15 6:46 AM, vidhya sankar wrote:
> > Dear justin Thank you for you reply
> >
> > Also when i use g_enemat tool as follows
> >
> >
> > g_enemat_d -f CNTPEPRSOLIONSfulllatest3.edr -groups group.dat -emat
> jnnff.xpm
> >
> > it shows the following error
> > Opened CNTPEPRSOLIONSfulllatest3.edr as single precision energy file
> > Will read groupnames from inputfile
> > Read 2 groups
> > group 0WARNING! could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE1
> (0,0)in energy file
> > WARNING! could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE2 (0,1)in
> energy file
> > group 1WARNING! could not find group (null):CYCLIPEPTIDE2-CYCLIPEPTIDE2
> (1,1)in energy file
> >
> > Will select half-matrix of energies with 6 elements
> > Last energy frame read 25000 time 50000.000
> > Will build energy half-matrix of 2 groups, 6 elements, over 25001 frames
> > Segmentation fault (core dumped)
> > though i set
> > 2
> > CYCLIPEPTIDE1
> > CYCLIPEPTIDE2as energy groups .my .mdp file whil running MD
> >
> > So why it shows error?
> >
>
> A seg fault is usually a bug.  There was a g_enemat seg fault in an old
> version,
> but it was fixed.  If you're not using 5.0.4, you should be.
>
> -Justin
>
> --
> ==================================================
>
> 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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