Re: [AMBER] frcmod file error

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Fri, 21 Oct 2016 12:42:29 -0300 (ARGSL-ST)

Hello,

Please, if you don't mind, follow the attached template to make your
desired cyclic peptide.-

Greeting,
Hector.



> Hi I have managed to make it cyclic by making bond in gaussian.
>
> But as soon as I am solvating it and making prmtop, inpcrd and pdb it
> seems that N terminal is breaking bond and making it -NH3
>
>
> I don't know why it is creating so much of trouble.
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Friday, October 21, 2016 1:43:38 AM
> To: david.case.rutgers.edu; AMBER Mailing List
> Subject: Re: [AMBER] frcmod file error
>
>
>>> 3. generate a reasonable starting structure for the cyclized peptide.
>> Amber is not a very good tool (generally speaking) for carrying out step
>> 3.
>>
> Though not the best at it, xleap will let you construct a cyclic
> peptide. In the cmd line:
>
> > mymol = sequence { ALA ALA .. ALA } # not a chemist btw
> > edit mymol
>
> And there get used to the controls so you can select the end atoms of
> the linear molecule one by one and and crudely move each out of line, so
> that you can draw a long bond between those atoms. Then select all the
> atoms, relax selection, all the weird bonds will be fixed as the
> molecule reforms, and with luck you are done, though iterative
> selection/relaxation might be needed if kinks develop. The energy
> minimization function is based on atom hybridizations, and lacks vdw.
>
> In the end you might want to have a more powerful and used molecular
> editor program at your fingertips, but xleap is there and once upon a
> time we put some time into making it work.
>
> Bill
>
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--------------------------------------
 Dr. Hector A. Baldoni
 Profesor Adjunto (FQByF-UNSL)
 Investigador Adjunto (IMASL-CONICET)
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
-.The theoretical approach these days can predict/show almost anything,
but the ultimate truth lies in the experiment.-

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Received on Fri Oct 21 2016 - 09:00:03 PDT
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