Of course a good check is also converting the topology from Gromacs to
Amber and double check parameters with ParmEd ... the more tests, the
better ...
Vlad
On 07/14/2016 12:28 PM, Vlad Cojocaru wrote:
> Dear Neha,
>
> My conservative, non-Gromacs user view is:
>
> If you want to run with Amber ff, I'd first choose Amber or NAMD
> (http://ambermd.org/namd/namd_amber.html) software .... Bottomline is:
> Amber software is most compatible with the AMBER ff, so using Amber
> software is the safest. For any other software you need to check
> carefully that you are using correct topologies and compatible running
> options (NAMD reads AMBER topologies and has some documented usage
> compatible with the Amber ff ... Gromacs does not read Amber topology
> but I believe Sorin's lab has the ffamber ports)
>
> If I am stuck with running the Amber ff in Gromacs, I'd do a careful
> test to see if the implementations of the Amber ff in Gromacs matches
> those in Amber (for those available in both) ... There are a number of
> ff versions available in both software packages that you could test
> for the numbers (single point energy calculations). If they match
> well, then probably you are safe to run Gromacs with Amber ff .. If
> they do not match, you probably need to contact the people
> implementing the Amber ff in Gromacs to make sure that you don't start
> off with artifacts ...
>
> Best
> Vlad
>
> On 07/14/2016 11:45 AM, Neha Gandhi wrote:
>> Dear Vlad,
>>
>> Thank you for your response. I am interested in simulating IDPs and most
>> force fields (ff03w, ff03ws, etc) are part of GROMACS package. In
>> terms of
>> enhanced sampling, in comes down to REMD, umbrella sampling or
>> metadynamics
>> in GROMACS. For a fairly medium size peptide, the computational
>> resources
>> are huge and one run isn't enough for checking the convergence. I am
>> interested in exploring aMD or gaMD first before reverting to other
>> sampling techniques, however as you rightly pointed out, we can
>> perform the
>> simulations with what is available.
>>
>> Regards,
>> Neha
>>
>> On 14 July 2016 at 17:56, Vlad Cojocaru
>> <vlad.cojocaru.mpi-muenster.mpg.de>
>> wrote:
>>
>>> Hi Neha,
>>>
>>> What you are saying argues against trusting conversion tools between
>>> Gromacs and Amber (its good you did a thorough test, but many don't do
>>> that) .... The thing is that if I am not mistaken all studies with
>>> ff99SB-ILDN* have been done using the Gromacs implementation which was
>>> probably done on top of the Gromacs implementation of ff99SB ... I have
>>> no idea how well the people that implemented these force fields in
>>> Gromacs tested them against Amber ... But you may be safest using also
>>> the Gromacs implementation ...
>>>
>>> We have been looking into using ff99sb-ildn* in amber for a while
>>> (example this thread and others:
>>> http://archive.ambermd.org/201409/0298.html) but we ended up using the
>>> Buschweiler's NMR-based modifications of ff99SB instead of the
>>> Best&Hummer mods. It worked for our purposes but we did not do any
>>> major
>>> tests on protein folding or secondary structure propensities ....
>>>
>>> At that time, Francesco Gervasio sent me his implementation of the
>>> ff99sb-ildn* force field in Amber but we could not use it because of
>>> some atom type incompatibilites (if I recall correctly, it was long
>>> ago)
>>> ....
>>>
>>> In the meantime we switched to the ff14SB (which is now published).
>>> However, some recent posts indicated some potential issues with the chi
>>> dihedrals in aromatic residues which apparently do not appear in ff12SB
>>> (its predecessor) ...
>>>
>>> So, my advice would be: unless you really depend on that particular
>>> force field, switch to what is available in Amber. There is probably no
>>> "one best force field" out there and you may find issue with any of
>>> them
>>> .... But using what is available in Amber for simulations with Amber
>>> topology is safer than conversions and adaptations.
>>>
>>> If you do insist on using ff99sb-ildn*, try to email Francesco Gervasio
>>> and maybe you can adapt his implementation .... Then, if you compare
>>> with Gromacs, you could also do a 1 energy point calculation with both
>>> Gromacs and Amber on 1 core and see if you get the same numbers ...
>>> (maybe its the topology conversion that fails)
>>>
>>> Best wishes
>>> Vlad
>>>
>>> On 07/14/2016 08:47 AM, Neha Gandhi wrote:
>>>> Dear List,
>>>>
>>>> I am sorry to bring up this query again on implementing ff99SB*-ildn
>>> which
>>>> was posted by some users in 2014 on the mailing list (
>>>> http://archive.ambermd.org/201409/0260.html).
>>>>
>>>> To reiterate, ff99SB*-ildn is available in GROMACS. I came across a
>>>> paper
>>>> (Biochemistry, 2016, 55 (12), pp 1784–1800) wherein they have
>>>> implemented
>>>> ff99SB*ildn in AMBER. It states "The potential associated with
>>>> dihedral
>>>> angle ψ has been corrected according to Best and Hummer;(14) the
>>> correction
>>>> has been applied to all residues, including Gly and Pro, same as in
>>> paper 1
>>>> (12) (we have verified that the outcome does not depend on whether the
>>>> correction is extended to glycines and prolines).”
>>>>
>>>> If I refer to reference 14 (Best and Hummer,2009), the
>>>> modifications are
>>>>
>>>> parameter
>>>> ff99SB**k*ψ (kcal/mol)
>>>> 0.1788δψ (deg)
>>>> 105.
>>>>
>>>> As a test, I tried preparing files in gromacs using ff99SB*-ildn
>>>> and then
>>>> converting to AMBER prmtop using gromber (parmEd). I also prepared
>>>> prmtop
>>>> file in AMBER using ff99SB-ildn for the same test peptide. However,
>>>> most
>>> of
>>>> the dihedral terms were strikingly different upon comparison in two
>>> files.
>>>> I could not figure out the modifications.
>>>>
>>>> I am not sure how to implement those modifications above using ParmEd?
>>> Do I
>>>> have to delete all dihedral terms first?
>>>>
>>>> Looking forward to your suggestions,
>>>>
>>>> Many thanks,
>>>> Neha
>>>> _______________________________________________
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>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> --
>>> Dr. Vlad Cojocaru
>>> Computational Structural Biology Laboratory
>>> Department of Cell and Developmental Biology
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Thu Jul 14 2016 - 04:00:02 PDT
