[gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)
Billy Williams-Noonan
billy.williams-noonan at monash.edu
Fri Jun 24 01:54:54 CEST 2016
Hi Mark,
I've consulted the GROMACS manual and I'm working on a few things. I
feel the explanations provided in the Hydrogen Database setion could be
aided with diagrams somehow. I'll have a look into people that have
topologies for b-alanine to save myself trying to get the formatting of the
forcefield files right. Thanks for your help... :)
Kind regards,
Billy
On 24 June 2016 at 08:34, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:
> Hi Mark,
>
> I noticed your paper from 2011 on parameter optimisation using EWALD
> and your position and GROMACS so I feel humbled to be talking with you.
>
> I have had a 'guess' at the topology for b-alanine (BAL) and added it
> to my aminoacids.rtp file in the gromos forcefield directory that I am
> using. My guess is based on the parameters for alanine, and I am assuming
> that what I have done would not be viable if two BAL residues were directly
> next to each other. Is what I have done correct and would it work?
>
>
> ;beta-alanine
>
> [ BAL ]
> [ atoms ]
> N N -0.3100 0
> H H 0.3100 0
> CA CH2 0.0000 1
> CB CH2 0.0000 1
> C C 0.4500 2
> O O -0.4500 2
> [ bonds ]
> N H gb_2
> N CA gb_21
> CA CB gb_27
> CB C gb_27
> C O gb_5
> C +N gb_10
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_32
> -C N CA ga_31
> H N CA ga_18
> N CA CB ga_13
> CA CB C ga_13
> CB C O ga_30
> CB C +N ga_19
> O C +N ga_33
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> CA N C CB gi_2
> C CB +N O gi_1
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_14
> -C N CA CB gd_44
> -C N CA CB gd_43
> CA CB C +N gd_45
> CA CB C +N gd_42
>
>
>
> When I run the command gmx pdb2gmx it gives me the following error:
>
> Fatal error:
> Atom OXT in residue BAL 7 was not found in rtp entry BAL with 6 atoms
> while sorting atoms.
>
>
> Additionally, it tells me this before the error message, while processing
> the command:
>
> Opening force field file ./gromos54a7_atb.ff/aminoacids.r2b
> Reading sim_lig_1.pdb...
> Read 60 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 7 residues with 60 atoms
>
> chain #res #atoms
> 1 'C' 7 60
>
> All occupancies are one
> Opening force field file ./gromos54a7_atb.ff/atomtypes.atp
> Atomtype 63
> Reading residue database... (gromos54a7_atb)
> Opening force field file ./gromos54a7_atb.ff/aminoacids.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing proper dihedrals found on the same bond as a
> proper dihedral
> Residue 109
> Sorting it all out...
> Opening force field file ./gromos54a7_atb.ff/aminoacids.hdb
> Opening force field file ./gromos54a7_atb.ff/aminoacids.n.tdb
> Opening force field file ./gromos54a7_atb.ff/aminoacids.c.tdb
> Processing chain 1 'C' (60 atoms, 7 residues)
> Identified residue TRP1 as a starting terminus.
> Warning: Residue BAL7 in chain has different type (Other) from starting
> residue TRP1 (Protein).
> Identified residue ASN6 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus TRP-1: NH3+
> End terminus ASN-6: COO-
>
>
>
> Apologies for the ignorance, but do you know what I need to do to fix this?
>
> Billy
>
>
>
> On 23 June 2016 at 17:44, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
>> Hi,
>>
>> There's a collection of contributed stuff on the GROMACS webpage, so good
>> luck with that... But mostly it's a matter of people choosing to share.
>> Authors of papers where such have been used should be willing to share
>> topology files.
>>
>> Mark
>>
>> On Thu, Jun 23, 2016 at 8:08 AM Billy Williams-Noonan <
>> billy.williams-noonan at monash.edu> wrote:
>>
>> > Hi Gromacs Users,
>> >
>> > Does anyone know where I can find a set of download-able parameters
>> for
>> > rare amino acids? Is there a repository of some kind?
>> >
>> > Kind regards,
>> >
>> > Billy
>> >
>> > --
>> > Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
>> >
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>
>
>
> --
> Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
> **|* +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>
--
Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|* +61420 382 557
Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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