[gmx-users] how to fit parameters for terminal residues in amber99sb-ildn?

[yoochan]

Dear Sangeun,

Sorry, I misunderstood your question.

As you mentioned, currently AMBER Force Field doesn’t support -NH2, -COOH parameters about terminal group.

I have no idea and I think it won’t be easy, unless you are not going to make new force fields using Antechamber(AMBER TOOL).

But why don’t you check previous case?
http://archive.ambermd.org/201003/0382.html <http://archive.ambermd.org/201003/0382.html>

Yoochan.

> On Apr 6, 2015, at 11:34 PM, sang eun jee <sangeunjee at gmail.com> wrote:
> 
> Hi Yoochan
> 
> Thanks for your reply.
> Actually my question was not specifically stating what I was really curious.
> 
> I know how to modify the library in AMBER99sb-ildn forcefield and pdb2gmx
> worked when I modified forcefield library in a right way. However, my goal
> is to simulate system with NH2 and COOH termini, not to simulate with
> capping termini via NME or other capping materials. What I wondered was, If
> I would like to include parameters for GLY with NH2 termini and HYP with
> COOH in amber99sb-ildn library, I need to know specific parameter values
> for those residues.
> 
> So, the question is, how can I derive parameters of GLY with NH2 termini
> once I know the parameters of the GLY residue at the center of the chan(N-H
> termini) and parameters of GLY with NH3 termini? Is there any specific rule
> to derive the parameters for specific termini?
> 
> Thank you very much,
> 
> Sangeun Jee
> 
> On Fri, Apr 3, 2015 at 9:54 PM, yoochan <yuchan.m at gmail.com> wrote:
> 
>> Dear Sangeun,
>> 
>> Did you try 'pdb2gmx' using your structure file?
>> 
>> I checked NME and NHE are in the AMBER99sb-ildn forecefield.
>> 
>> So, if pdb2gmx doesn't work, you can draw NME and NHE using molecular
>> viewer and then change residue/atom name to NME and NHE.
>> 
>> 
>> Yoochan
>> 
>> 
>> 
>>> On Apr 4, 2015, at 7:01 AM, sang eun jee <sangeunjee at gmail.com> wrote:
>>> 
>>> Dear  gromacs users
>>> 
>>> Hello. I have question how to decide terminal residue forcefield and put
>>> them in library?
>>> 
>>> I am using AMBER99sb-ildn forcefield in gromacs. Not like gromos or opls
>>> forcefield, amber forcefield treat termini in its own way and current
>>> version only works with NH3+ and COO-. I would like to termini as a
>> neutral
>>> status, NH2 and COOH and would like to modify forcefield to include this
>>> specific termini data.
>>> 
>>> To decide charges and parameters to describe specific termini, is there
>> any
>>> way to decide parameters based on non-terminal residue database? When I
>>> looked at NGLY and GLY from animoacids.rtp,  I could not find out
>> specific
>>> rules.
>>> 
>>> Thank you very much.
>>> 
>>> Sangeun Jee
>>> --
>>> Post Doctoral Researcher
>>> School of Materials Science and Engineering
>>> Georgia Institute of Technology
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> 
> 
> 
> -- 
> Post Doctoral Researcher
> School of Materials Science and Engineering
> Georgia Institute of Technology
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