AMBER Archive (2009)

Subject: Re: [AMBER] RE:xleap problem

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Mon Jan 26 2009 - 14:47:26 CST

oguz gurbulak wrote:
> Dear D Case,
>
> I again run some experiments according to your advices and my
> min.out file is like in below. I used packmol, I wrote box size for
> x, y, z : 9.825 A and created a packmol pdb file for this system. So
> I didn't use solvatebox command in xleap. I thought that there is a
> problem about using packmol. If so, How can I solve this problem and
> use packmol without any errors ? In this sense, I'm waiting for your
> help and also other people's help who have enough experience on
> PACKMOL package. Or I'm waiting for some alternative solutions of
> you related with LEAP.
>
> Sincerely,
>
> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 10
>
> | Run on 01/26/2009 at 15:55:22
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: /home_palamut2/ogurbulak/c7AMBER10/min/min.in
> | MDOUT: /home_palamut2/ogurbulak/c7AMBER10/min/min.out
> | INPCRD: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.inpcrd
> | PARM: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.prmtop
> | RESTRT: /home_palamut2/ogurbulak/c7AMBER10/min/n-dodecane.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> | MDINFO: mdinfo
> |LOGFILE: logfile
>
>
> Here is the input file:
>
> initial minimization
> &cntrl
> imin=1,
> maxcyc=500,
> ncyc=250,
> ntb=1,
> cut=9.825,
> ntpr=100,
> ntc=2, ntf=2,
> /
>
> | ERROR: Box parameters not found in inpcrd file!
>

Sorry to break into this thread, but I think there is a problem with
packmol-generated pdb files. The individual molecules need a TER card
between them, and packmol leaves the TER cards out. There was a
script posted to the email list to insert them automatically, but I
can't find the copy I made from the email.

If this causes anyone to remember, please repost the script.

Did leap finish without errors? Did it complain about the lack of
TER records?

By the way, it would be a help if you used gzip or some standard
compression program to compress files posted to the list. Some of us
do not have a program to handle these rar files. What are they? It
is identified by file(1) as
"inpcrd.rar: RAR archive data, v14, os: Win32"

Bud Dodson 

-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one

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