Mr Bernard Ramos wrote:
Thank you, sir. That's nice of Gromacs to automatically assign new atom
types from an input pdb file. I check out the link as well.
To be clear, an atomtype is only assigned if:
1. it is present in the .atp
2. it has relevant parameters assigned in ffnonbonded.itp (and possibly
ffbonded.itp if it is involved in bonded interactions, as well)
3. it is utilized in a building block defined in the .rtp file, and
4. an atom with a name corresponding to that of the .rtp entry is found in the
input coordinate file
All conditions must be satisfied for the resulting topology to be useful (or
produced at all, for that matter).
-Justin
--- On *Mon, 2/21/11, Justin A. Lemkul /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] on force fields
To: "Discussion list for GROMACS users" <[email protected]>
Date: Monday, February 21, 2011, 10:41 AM
Mr Bernard Ramos wrote:
> Thanks for the reply on my first querry. I have another one. If I
add a NEW atom type in *.atp file, will Gromacs automatically
recognize this atom type?
Theoretically, yes, provided that you supply any corresponding
parameters in, e.g., ffnonbonded.itp and ffbonded.itp. However,
there is an unresolved bug related to atomtype assignment that may
be relevant:
http://redmine.gromacs.org/issues/618
It seems to me that any alterations to the .atp file cause things to
break down, so do not be surprised if there are problems.
-Justin
> Thanks.
>
>
> --- On *Wed, 2/16/11, Mark Abraham /<[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>/*
wrote:
>
>
> From: Mark Abraham <[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> Subject: Re: [gmx-users] on force fields
> To: "Discussion list for GROMACS users"
<[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> Date: Wednesday, February 16, 2011, 1:53 PM
>
> On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote:
>> Hi everyone!
>> I need to update the gromos force field 53A6 with the
new force
>> field 53ACARBO (JCC 10 NOV 2010).
>> 1. I will have to change the parameter values in the file
>> ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are
these
>> the only files that I need to update if I need to switch to
a new
>> force field?
>>
>
> You should make a copy of the whole force field directory
into your
> working directory, rename the new directory suitably, make a
> suitable change to forcefield.doc, and then edit .itp files
> suitably. This means you're leaving your reference version
untouched
> and can edit locally to your heart's content, and can be sure
you're
> selecting the right force field with pdb2gmx and/or in your
.top file.
>
>> 2. The new force field 53ACARBO has a new gromos
functional form
>> for select torsional potentials. How to I go over implementing
>> this in gromos?
>>
>
> Preferably as a sum of existing functional forms. Or use
tabulated
> bonded interactions (see manual and wiki).
>
> Mark
>
> -----Inline Attachment Follows-----
>
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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