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
>>> _______________________________________________
>>> 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
>>
>>
>> _______________________________________________
>> 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 - 03:30:02 PDT
