Hello Pengfei,
Thanks for your e-mail.
In fact, I figured it out myself. There wasn’t one problem in the input file, but many.
One important to be noted was that the charges in the c4file.dat must have been surely integer whereas mine was -1.2!
Anyhow, it works like a charm now. Thanks a lot for your concern.
Bests,
/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
From: Pengfei Li
Sent: Tuesday, 12 June 2018 22:12
To: AMBER Mailing List
Cc: Qinghua Liao
Subject: Re: [AMBER] Including C4 terms LJ12-6-4
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 Wed Jun 13 2018 - 04:30:02 PDT
