Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10

From: Keith Van Nostrand <kifvan.yahoo.com>
Date: Thu, 16 Jul 2009 22:08:04 +0100

Ross and Amber Users,

  I have double checked that I am using the addles that came with Amber 10.  A fresh checkout of Amber 10 was done yesterday and recompiled with the same results.
  I notice that the top of the addles output says:

 AMBER8 Module: addles
 set up Locally Enhanced Sampling topology

  Despite it being Amber 10.  I also checked my reactant.prmtop (input single-image prmtop file) to make sure that was generated with the latest version of tleap, and it appears it has.  The top of the prmtop file reads:

%VERSION  VERSION_STAMP = V0001.000  DATE = 05/27/09  14:22:03
%FLAG TITLE
%FORMAT(20a4)
%FLAG POINTERS
%FORMAT(10I8)
     587      14     201     432     453     672    1012    1227       0       0
    3262      18     432     672    1227      35      72      40      24       0
       0       0       0       0       0       0       0       0      34       0
       0

  Is it possible I am still using an outdated version of addles despite getting the latest code?  I also applied the latest bugfixes.
  What is the difference between the Amber9 and Amber10 prmtop files?  I have followed the instructions in the manual, but have found no other guidance regarding Amber10 NEB or QMMM NEB.

Sincerely,
Keith Van Nostrand





________________________________
From: Ross Walker <ross.rosswalker.co.uk>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, July 10, 2009 12:21:11 PM
Subject: RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10

Hi Keith,

Just to check. You are using AMBER 10 Addles to create the prmtop file for the AMBER 10 NEB? The approach used changed between AMBER 9 and AMBER 10 so AMBER 9 NEB prmtop's will not work with AMBER 10 and vice versa.

All the best
Ross

> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Keith Van Nostrand
> Sent: Friday, July 10, 2009 8:27 AM
> To: amber.ambermd.org
> Subject: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using
> Amber10
>
> Amber List,
>
>  I am attempting to run QM/MM NEB with PM3-PDDG on an RNA system with
> Amber 10.
>
>  Inpcrd files for the starting and ending configuration are each
> copied 15 times to give a total of 30 images.
>
>  My addles.in file is as follows:
>
> file rprm name=(reactant.prmtop) read
> file rcrd name=(cat_reactant15X-product15X.inpcrd) pack=30 read
> file wprm name=(AA-NEB-30image.prmtop) wovr
> file wcrd name=(AA-NEB-30image.inpcrd) wovr
> action
> omas
> pimd
> spac numc=30 pick #prt 1 587 done
> *EOD
>
>
>  My .in file is as follows:
>
> NVT MD w/ position restraints (5 kcal/molA) and PME (sander)
>  &cntrl
>  nmropt = 0,
>  ntx    = 1,      irest  = 0,
>  ntpr  = 50,      ntwx  = 50,
>  ntf    = 2,      ntb    = 0,      dielc  = 1,
>  igb    = 1,
>  cut    = 15.0,    saltcon= 0 , rgbmax =15.0,
>  imin  = 0,
>  maxcyc = 5000,
>  ncyc  = 1000,
>  dx0    = 0.1,    dxm    = 0.5,    drms  = 0.0001,
>  nstlim = 1000,
>  nscm  = 1000,
>  t      = 0,  dt    = 0.002,
>  temp0  = 300.0,  tempi  = 300,
>  ig    = 1000,
>  ntt    = 3,
>  gamma_ln  = 100,
>  vlimit = 20.0,
>  ntp    = 0,      pres0  = 1.0,
>  ntc    = 2,
>  ineb = 1,
>  skmin = 10, skmax = 10, tmode = 1,
>  ifqnt = 1
> /
>  &qmmm
>  qmmask = '.143-156,437-450',
>  qmcharge = 0,
>  qmcut = 8.0, qmshake = 0,
>
>  qm_theory = 'PM3-PDDG', verbosity = 0,
>
>  printcharges = 0, peptide_corr = 0,
>
>  writepdb = 1,
>  dftb_disper = 0
> /
>  &end
>
>
>  I attempt to run the calculation on a linux cluster with amber10
> sander.MPI and get the following error at the end of the output file:
>
> | Flags: MPI
>  *** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
>      THAT WERE CREATED BY ADDLES, WITH NPARM=1
>      USE A VERSION COMPILED WITH –DLES
>
>
>  I suspect the problem may be with addles and the prmtop file.  The
> same procedure with addles has worked for amber9 NEB using an MM force
> field.  I attempted to submit this above calculation using only the MM
> force field as well with amber10 and get the same error in the .out
> file, so I don’t think this problem is related to the QMMM settings.
>
>  Does anyone have suggestions on how I may get PM3-PDDG QMMM NEB to
> work?
>
> Sincerely,
> Keith  Van Nostrand
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


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Received on Thu Jul 16 2009 - 18:08:54 PDT
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