AMBER Archive (2006)

Subject: Re: [Fwd: AMBER: Long line of input]

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Jul 25 2006 - 11:08:27 CDT

Thank you all,

I have solved the problem by recompiling the source code, findmask.f
(80 to 200).

Have a nice day.

On 7/24/06, Viktor Hornak <hornak_at_csb.sunysb.edu> wrote:
> Myunggi,
>
> sorry for taking a while to respond but what you might need to do is
> change all occurrences of number "80" in a file
> $AMBERHOME/src/sander/findmask.f to "250" and recompile sander. That
> should fit your restraintmask which is about 120 characters long. One
> would think that the default buffer for the string should be made even
> larger but I think that the fortran namelist input mechanism has
> inherent limits at 256 characters or so and it probably wouldn't work.
> Let me know if you still don't know what you should do.
>
> -Viktor
>
> -------- Original Message --------
> Subject: AMBER: Long line of input
> Date: Wed, 19 Jul 2006 16:13:26 -0400
> From: Myunggi Yi <myunggi_at_gmail.com>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
>
>
>
> Dear Amber users,
>
> I'm trying to apply harmonic restraint.
> How can I solve the problem of long line input?
> The following is my input.
>
> ============================
> npt
> &cntrl
> nstlim = 50000, dt=.002,
> irest=1, ntpr=500, ntwx=500, ntx=5,
> temp0=310.0, ntt=1,
> tautp=0.4, taup=0.6, cut=9.0,
> ntb=2, ntp=2, iwrap=1,
> ntc=2, ntf=2,
> ntr=1, restraint_wt=5.0,
> restraintmask='(:1-108 & !@H=) |
> :110,111,114,117,119,120,124,125,128,134,137,138,140,142,148-152,154,155,176,178,180,182,204,213,215_at_P',
> itgtmd=1,
> tgtrmsmask=':1-108 & !@H=',
> /
> ============================
>
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
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>
> --
> ===================================================================
> Viktor Hornak
> Center for Structural Biology Phone: (631)632-1439
> SUNY at Stony Brook Fax: (631)632-1555
> Stony Brook, NY 11794-5115 E-mail: viktor.hornak_at_sunysb.edu
> ===================================================================
>
> 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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