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

Ming Tang m21.tang at qut.edu.au
Thu Apr 30 15:49:43 CEST 2015


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.
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
> 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 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

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