Dear Neha,
you might want to take a look at "An Updated Test of AMBER Force Fields
and Implicit Solvent Models in Predicting the Secondary Structure of
Helical, β-Hairpin, and Intrinsically Disordered Peptides", J. Chem.
Theory Comput., 2016, 12 (2), pp 714–727
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b01211
Best regards
Alessandro
Il 14/07/2016 11:45, Neha Gandhi ha scritto:
> 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
>>
>
>
--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
skype alessandrocontini
http://www.scopus.com/authid/detail.url?authorId=7003441091
http://orcid.org/0000-0002-4394-8956
http://www.researcherid.com/rid/F-5064-2012
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Received on Thu Jul 14 2016 - 03:00:05 PDT
