Could you post the error that you get?
Best,
Callum
________________________________
From: Vijay Achari <glycoamber.gmail.com>
Sent: Thursday, August 16, 2018 8:26:46 AM
To: AMBER Mailing List
Subject: Re: [AMBER] alkyl chain unsaturated bond
Thanks for the reply.
Well, I tried to model glycoside (mannose + alkyl chain with unsaturated
chain).
For the mannose I used GLYCAM_06j.dat force field, For the lipid I used
lipid17.dat
With the help of gafft2 and above mentioned force fields I am able to write
the bond, and angle values.
When I check in the xleap, there is no error.
But when I tried to generate topology and coordinate files using
"saveamberparm" command, I get a long list for the torsion angle where
amber try to fix and at the end it says
error and can not save the topology and coordinate files.
How I should go about this?
I used Ambertools18
Thanks
On Mon, Aug 13, 2018 at 10:03 PM, Dickson, Callum <
callum.dickson.novartis.com> wrote:
> I believe C5=C6 should be atom type cB and their respective hydrogens
> should be hB. You can check $AMBERHOME/dat/leap/parm/lipid14.dat to look
> at the atom types.
>
>
> Best,
>
> Callum
>
> ________________________________
> From: Vijay Achari <glycoamber.gmail.com>
> Sent: Sunday, August 12, 2018 5:58:42 PM
> To: AMBER Mailing List
> Subject: [AMBER] alkyl chain unsaturated bond
>
> Dear Amber experts,
>
> I am using AMBER14, with loading force files *leaprc.ff12SB, GLYCAM06_j, *
> and* lipid14.dat*
>
> I need some help on choosing correct atom type for carbons in aliphatic
> chain with a unsaturated bond.
>
> My aliphatic chain as below:
>
> *-C4-C5=C6-C7-*
>
> The *C4 & C7* are connected to two aliphatic hydrogen atoms each. *C5 & C6*
> connected by a double bond and each carbon connected to a single hydrogen.
>
> I used atom type cA for C4 & C7 carbons and hA atom type for the four
> hydrogen atoms which are connected to C4 & C7.
>
> *I am not sure what "atom type" to use for C5 & C6 which connected via a
> double bond and to the respective hydrogen atoms.*
>
> I appreciate a help for this problem.
>
> Thanks.
>
> Vijayan
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Received on Thu Aug 16 2018 - 07:30:03 PDT
