Hi Pooria,
.CR6 means the atom which has a name of CR6 not the residue which has a name of CR6.
I cced this email to Qinghua and I think he knows better about how to deal this issue since he is the first author of this paper: J. Phys. Chem. Lett. 2017, 8, 5408-5414.
-Pengfei
> On Jun 12, 2018, at 8:41 AM, Pooria Farahani <pooriaf.kth.se> wrote:
>
> Dear Amber troupe,
>
> I desperately need your help/suggestions.
> We are trying to include C4 terms for Lennard-Jones (12-6-4), using parmed command. However applying the following input file gives zero C4 numbers!!!!
> The input is as follows.
> -------------------------------------------------
> loadRestrt mol.inpcrd
> setoverwrite true
> add12_6_4 .CR6 c4file c4file.dat polfile lj_1264_pol.dat
> outparm mol2.prmtop mol2.inpcrd
> printDetails :CR6
> printLJMatrix :CR6
> quit
>
> Also the C4 values are coming from J. Phys. Chem. Lett. 2017, 8, 5408-5414.
> And the file for C4 is as follows.
> -------------------
> Cr-1.2 180
> D+0.7 0
> -------------------
> The name for the residue in PDB file is CR6. But instead of C4 180 the parmed command generates 0. The command I have applied is:
>>>> parmed -p mol.prmtop -c mol.inpcrd -i parmed.in
>
>
> Does anyone have a clue?
> Would you mind please helping me to proceed?
>
> You are so appreciated to consider and help.
>
> Cordially,
> /Pooria
>
>
>
> Pooria Farahani, PhD Researcher,
> Division of Theoretical Chemistry & Biology,
> School of Biotechnology, KTH Royal Institute of Technology,
> Roslagstullsbacken 15,
> SE-10691, Stockholm, Sweden
> Cell: +46 707 99 30 69
> E-mail: pooriaf.kth.se
> https://www.kth.se/profile/pooriaf?l=en
>
>
>
>
> ---
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Received on Tue Jun 12 2018 - 13:30:03 PDT
