Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue May 17 2016 - 11:43:05 CDT

Thanks, I found uneasy going by analogy in this case (may be I am wrong)
so that I am already advanced with QM calculations

francesco pietra

On Tue, May 17, 2016 at 4:29 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> This is a pretty rare case, a single amino acid terminated on both ends,
> so it’s not surprising that it was overlooked in the parameter file.
> However, you should be able to easily identify appropriate parameters by
> analogy.
>
> Best,
> JC
>
> On May 16, 2016, at 9:54 AM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
> Dear Peter:
> yes, I made that clear. Apparently, to my disappointment, NNEU was not
> accompanied by appropriate parameters for atom C being terminal.
>
> all the best
> francesco
>
> On Mon, May 16, 2016 at 2:46 PM, Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Dear Francesco,
>> The lines that you quoted from the prm file are for angles centered on
>> CC, but the angle that namd is complaining about is centered on CT1. These
>> are not the same thing…
>> Best,
>> Peter
>> >
>> > On Mon, May 16, 2016 at 9:45 AM, Francesco Pietra <
>> chiendarret_at_gmail.com> wrote:
>> > Hello:
>> > By using VMD in text mode (psfgen) with CHARMM36, I am getting error in
>> MD (NAMD2.11):
>> >
>> > ERROR: Unable to find angleparams for CC CT1 NH2 (atoms 2971 2974 2980)
>> >
>> > Actually, ID/atomtype is
>> >
>> > 2971 NH2
>> >
>> > 2974 CT1
>> >
>> > 2980 CC
>> >
>> > for a CYS ligand made NH2 with PRES NNEU.
>> > ------------------
>> >
>> > In used top_all36_prot.prm, angleparams for
>> >
>> > NH2 CC CT1
>> >
>> > NH2 CC CT2
>> >
>> > NH2 CC CT3
>> >
>> > do exist.
>> > ----------------------
>> >
>> > Thanks for advice
>> >
>> > francesco pietra
>> >
>> >
>> >
>> > Could the issue arise from having
>> >
>>
>>
>
>

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