You can convert both topology and coordinate files from amber to gromacs
format.
The errors associated with this are described here:
https://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
HTH
On Mon, Aug 12, 2013 at 3:32 PM, Golshan Hejazi <golshan.hejazi.yahoo.com>wrote:
> Thanks guys for the helps and suggestions.
>
> Ross, I am using Metadynamics and it is faster on gromacs. I don't know
> how the PLUMED and other stuff could be lunched on AMBER. That forces me to
> use gromacs. I will consider your suggestion on how to hack the script for
> printing with higher precision.
>
> Oliver, it seems this script is for the topology file. Sure it is better
> to use the latest version but as you see the problem that I was dealing
> with is related to the coordinate file and I think we have to take into
> account these kind of simple checks about the bond, angle and dihedrals
> while converting to gromacs.
>
> G.
>
> ------------------------------
> *From:* Oliver Grant <olivercgrant.gmail.com>
>
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Cc:* Golshan Hejazi <golshan.hejazi.yahoo.com>
> *Sent:* Saturday, August 10, 2013 5:26 AM
>
> *Subject:* Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy
> between amber and gromacs
>
> Hi all,
> acpype is probably what you want to be using for converting amber to gmx:
> https://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs
> It's been updated a lot more than the perl script.
> I don't use it though so I'm not aware of any quirks or if it's able to
> handle ACE and NME correctly.
>
>
>
> On Sat, Aug 10, 2013 at 12:42 AM, Ross Walker <ross.rosswalker.co.uk>wrote:
>
> Hi Golshan,
>
> I don't know of any other converters one could use - or even if Gromacs
> will
> accept more than 3 decimal places for the input coordinates. If it does
> then
> I'd suggest trying to hack the conversion script to print more decimal
> places. If it doesn't then the alternative (for doing sanity checks that
> the
> script is working) would be to quickly write something that zeros the amber
> inpcrd coordinates after the second decimal place.
>
> The real place I'd be wary that things are working or not is in the non
> bonds, so VDW and EEL which might be harder to compare since you have to do
> quite a bit of work to get the exact same calculation setup - but at least
> checking the dihedrals is a good initial sanity check.
>
> And who 'forces' you to use Gromacs? - You should switch to AMBER, get a 4
> x
> GPU machine and you'll be able to run WAYYYY more sampling than you can
> with
> Gromacs. E.g. a 4-way GTX-Titan machine from Exxact can run 4 JAC-NVE runs
> at 111ns/day each so you get almost 450ns/day of aggregate throughput.
> Gromacs won't even get you close to that on such a machine.
>
> All the best
> Ross
>
> From: Golshan Hejazi <golshan.hejazi.yahoo.com>
> Reply-To: Golshan Hejazi <golshan.hejazi.yahoo.com>
> Date: Friday, August 9, 2013 3:32 PM
> To: Ross Walker <ross.rosswalker.co.uk>, AMBER Mailing List
> <amber.ambermd.org>
> Subject: Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between
> amber and gromacs
>
> Ross, thanks a lot. I really appreciate your effort to clarify the source
> of
> problem. This was so Nasty!!!!
> I did exactly the same calculation, but I used the coordinate of gromacs
> ...!!!
>
> In fact, I checked and luckily, the different energy of two structure are
> comparable in gromacs and amber ... regardless that the absolute value of
> energies are not matching !!!
>
> So, at this point, what is your suggestion! I am forced to use gromacs ...
> but I will use amber force fields. Do you know of any better converter ...!
>
> Any suggestion will help :)
>
> Best
> G.
>
>
>
>
>
>
>
> From: Ross Walker <ross.rosswalker.co.uk>
> To: Golshan Hejazi <golshan.hejazi.yahoo.com>; AMBER Mailing List
> <amber.ambermd.org>
> Sent: Friday, August 9, 2013 5:54 PM
> Subject: Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between
> amber and gromacs
>
>
>
> Ok, here's what I get for AMBER.
>
> 1) Using RDPARM to get the bond info ($AMBERHOME/bin/rdparm
> ALA-amber.top bonds)
>
> Bond Kb Req atom names (numbers)
> 1: 434.00 1.010 :1.N :1.H (1,2)
> 2: 340.00 1.090 :1.CA :1.HA (3,4)
> 3: 340.00 1.090 :1.CB :1.HB1 (5,6)
> 4: 340.00 1.090 :1.CB :1.HB2 (5,7)
> 5: 340.00 1.090 :1.CB :1.HB3 (5,8)
>
> 6: 337.00 1.449 :1.N :1.CA (1,3)
> 7: 310.00 1.526 :1.CA :1.CB (3,5)
> 8: 317.00 1.522 :1.CA :1.C (3,9)
> 9: 570.00 1.229 :1.C :1.O (9,10)
>
>
>
>
> Then for the structure you provided going through each bond in turn:
>
> sqrt([Xi-Xj]^2+[Yi-Yj]^2+[Zi-Zj]^2)
>
> 1 - 3.3257700 1.5479090 -0.0000016 3.9094070 0.7236110 -0.0000027
> = 1.010
> 2 - 3.9700480 2.8457950 -0.0000001 3.6716630 3.4001290 -0.8898200
> = 1.090
> 3 - 3.5769650 3.6538380 1.2321430 3.8774840 3.1157950 2.1311970 = 1.090
> 4 - 3.5769650 3.6538380 1.2321430 4.0750590 4.6230170 1.2057860 = 1.090
> 5 - 3.5769650 3.6538380 1.2321430 2.4969950 3.8010750 1.2413790 = 1.090
> 6 - 3.3257700 1.5479090 -0.0000016 3.9700480 2.8457950 -0.0000001 = 1.449
> 7 - 3.9700480 2.8457950 -0.0000001 3.5769650 3.6538380 1.2321430 = 1.525
> 8 - 3.9700480 2.8457950 -0.0000001 5.4855410 2.7052070 -0.0000044 = 1.522
> 9 - 5.4855410 2.7052070 -0.0000044 6.0088240 1.5931750 -0.0000084 = 1.229
>
> So then we have
>
> Ebond = kr(r - req)^2
>
> the ONLY bond here that is not at it's equilibrium bond length is 7 which
> is 1.525 vs 1.526
>
> Hence the total bond energy is 310.0 * (1.525 - 1.526)^2 = 0.00031 Kcal/mol
>
> Which is exactly what AMBER is reporting. So I'm not sure how you got the
> values you did for the AMBER calculation.
>
> Now, looking at your gromacs coordinates:
>
> 1ALA N 1 0.333 0.155 -0.000
> 1ALA H 2 0.391 0.072 -0.000
> 1ALA CA 3 0.397 0.285 -0.000
> 1ALA HA 4 0.367 0.340 -0.089
> 1ALA CB 5 0.358 0.365 0.123
> 1ALA HB1 6 0.388 0.312 0.213
> 1ALA HB2 7 0.408 0.462 0.121
> 1ALA HB3 8 0.250 0.380 0.124
> 1ALA C 9 0.549 0.271 -0.000
> 1ALA O 10 0.601 0.159 -0.000
>
> We first see that the coordinates are horribly truncated at 3 decimal
> places. So I think what you are seeing is that the coordinate file being
> spat out by the conversion script is extremely low precision and this is
> what is causing your problems. Nasty.
>
>
> All the best
> Ross
>
>
> On 8/9/13 10:02 AM, "Golshan Hejazi" <golshan.hejazi.yahoo.com> wrote:
>
> >Dear Adrian,
> >
> >Thanks for the correction. I computed by hand!!!! for amber and gromacs
> >the BOND energy of ALA according to amber topology.
> >Here is the results:
> >
> >GROMACS:
> >The number that I obtained: .440148 (kj/mol)
> >The number in the gromacs log file: .220074 (kj.mol)
> >
> >There is a factor of 2 difference ... which I think it is correct ... and
> >they take care of it in the energy file.
> >
> >AMBER:
> >The number that I obtained: .052598574280 (kcal/mol)
> >The number in the AMBER mdout file: 0.0003 (kcal/mol)
> >
> >
> >What is really the correct value? I think .220074 (kj.mol) is the correct
> >value ... because when I convert it to kcal/mol ... I arrive to the same
> >number .052598574280 (kcal/mol) ... that I obtained by manually
> >computing the BOND energy for amber.
> >
> >I attached some files if you wish to control it. There is crd and top
> >file of amber, gro and top file of gromacs and another file(called test)
> >which contains to make it easier for you to check:
> >
> >r_eq r(distance of the atom according to amber.coor) k(gromacs)
> >k(amber)
> >
> >What do you think?
> >
> >G.
> >
> >
> >
> >
> >________________________________
> > From: Adrian Roitberg <roitberg.ufl.edu>
> >To: Golshan Hejazi <golshan.hejazi.yahoo.com>; AMBER Mailing List
> ><amber.ambermd.org>
> >Sent: Friday, August 9, 2013 11:05 AM
> >Subject: Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between
> >amber and gromacs
> >
> >
> >Why would you do
> >
> >sum (ki*(r_i*r_i)) ??
> >
> >
> >That is not the correct equation. What you need is k*(r_i - r_re_i)**2,
> >which is the difference between the actual bond lengths minus the
> >equilibrium value.
> >
> >
> >On 8/9/13 10:53 AM, Golshan Hejazi wrote:
> >> This is for ALA to avoid any complication!
> >>
> >>
> >> [ bonds ]
> >> ; ai aj funct r k
> >> 1 2 1 1.0100e-01 3.6317e+05
> >> 3 4 1 1.0900e-01 2.8451e+05
> >> 5 6 1 1.0900e-01 2.8451e+05
> >> 5 7 1 1.0900e-01 2.8451e+05
> >> 5 8 1 1.0900e-01 2.8451e+05
> >> 1 3 1 1.4490e-01 2.8200e+05
> >> 3 5 1 1.5260e-01 2.5941e+05
> >> 3 9 1 1.5220e-01 2.6527e+05
> >> 9 10 1 1.2290e-01 4.7698e+05
> >>
> >> >From here, I computed manually the bond energy which is : sum
> >>(ki*(r_i*r_i)) = 42536.87 (kj/mol)
> >> however, when I perform a rerun on the gro file ... this is the bond
> >>energy: 2.20074e-01 (kj/mol) in gromacs
> >> and 0.0003 (kcal/mol) from amber
> >>
> >>
> >>
> >> ________________________________
> >> From: David A Case <case.biomaps.rutgers.edu>
> >> To: Golshan Hejazi <golshan.hejazi.yahoo.com>; AMBER Mailing List
> >><amber.ambermd.org>
> >> Sent: Friday, August 9, 2013 9:46 AM
> >> Subject: Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy
> >>between amber and gromacs
> >>
> >>
> >> On Fri, Aug 09, 2013, Golshan Hejazi wrote:
> >>> I computed the BOND and ANGLE energies. But it is only increasing my
> >>> confusion ... Look: I have a simple ace-ala-nme system.
> >> How about going to just ace-nme? It would much easier to compare each
> >> individual term, and you would still have bonds, angles and dihedrals.
> >>
> >> While I am thinking about it, be sure that the conversion of the
> >>blocking
> >> groups (ace and nme) between Amber and Gromacs is correct (i.e. not just
> >> the amino acids themselves.)
> >>
> >> ...dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >--
> > Dr. Adrian E. Roitberg
> >
> >Colonel Allan R. and Margaret G. Crow Term Professor.
> >Quantum Theory Project, Department of Chemistry
> >University of Florida
> >roitberg.ufl.edu
> >352-392-6972
> >
> >
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >
> http://lists.ambermd.org/mailman/listinfo/amber___________________________
> >____________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
>
>
>
>
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>
>
>
>
> --
> Oliver Grant
> PhD Student,
> Computational Glycoscience Laboratory,
> School of Chemistry,
> National University of Ireland, Galway
>
>
>
--
Oliver Grant
PhD Student,
Computational Glycoscience Laboratory,
School of Chemistry,
National University of Ireland, Galway
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Received on Sat Aug 17 2013 - 06:00:03 PDT
