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Is it possible I am still using an outdated version of addles despite getting the latest code?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
>
>
>
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Received on Thu Jul 16 2009 - 18:08:54 PDT
