Re: minimization problem

From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Tue Aug 09 2011 - 08:21:37 CDT

Hi,
Thanks for the reply. I used a vmd tool for the creation of psf file.
I used the lammpsdatafile to create a psf file. Hence i dont have any topology file.

Sincerely
Naresh
> ----------------------------------------
> From: Jeffrey Potoff <jpotoff_at_chem1.eng.wayne.edu>
> Sent: Tue Aug 09 14:16:08 CEST 2011
> To: NAMD <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: minimization problem
>
>
> That's the parameter and PSF file. Where is your topology file?
>
> On 8/9/2011 8:00 AM, Narasimhan LOGANATHAN wrote:
> > Hi all,
> > I have attached the parameter and topology file along with this.
> > Could you help me to overcome the problem of splitPatch hydrogen
> >
> >
> > bond o* h* 554.1349 1.0000 ! water
> >
> > angle h* o* h* 45.7696 109.47 ! water
> >
> > ! atom eps sigma eps (1:4) sigma(1:4)
> > ! type (kcal/mol) (A)
> > ! --------------------------------------------------------------
> > NONBonded h* 0.0000 0.0000 0.0000 0.0000
> > NONBonded ho 0.0000 0.0000 0.0000 0.0000
> > NONBonded o* 0.1554 3.1655 0.1554 3.1655
> >
> > PSF
> >
> > 1 !NTITLE
> > REMARKS VMD generated structure x-plor psf file
> >
> > 2520 !NATOM
> > 1 0 1 1 0.410000 1.0079 0
> > 2 0 1 1 0.410000 1.0079 0
> > 3 0 2 2 -0.820000 15.9994 0
> > 4 0 1 1 0.410000 1.0079 0
> > 5 0 1 1 0.410000 1.0079 0
> > 6 0 2 2 -0.820000 15.9994 0
> >
> > 840 !NTHETA: angles
> > 4 3 5 7 6 8 1 9 2
> > 13 12 14 10 15 11 19 18 20
> > 16 21 17 25 24 26 22 27 23
> > 31 30 32 34 33 35 28 36 29
> > 40 39 41 37 42 38 46 45 47
> > 43 48 44 52 51 53 49 54 50
> > 58 57 59 61 60 62 55 63 56
> > 67 66 68 64 69 65 73 72 74
> > 70 75 71 79 78 80 76 81 77
> >
> >
> > 0 !NPHI: dihedrals
> >
> >
> > 0 !NIMPHI: impropers
> >
> >
> > 0 !NDON: donors
> >
> >
> > 0 !NACC: acceptors
> >
> >
> > 0 !NNB
> >
> > Regards
> > Naresh
>
>
> --
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>

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