Did you change the path in your script as well? What command line did you start leap with?
Bill
<div>-------- Original message --------</div><div>From: "Dey, S." <s.dey.student.rug.nl> </div><div>Date:07/18/2017 2:11 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] Error in LEaP </div><div>
</div>Hi Abhishek,
I also thought of the same. So, I brought the leaprc.gaff file into my
working directory and then ran leap. But, it keeps showing the same error.
Souvik
On Mon, Jul 17, 2017 at 6:02 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi Sauvik,
>
>
> see you have errors
>
> *(no leaprc in search path)*
>
> *: not foundpen file leaprc.gaff*
>
>
> So to me, it seems the path that you are giving to load leaprc.gaff is
> wrong.
>
> kindly check it.
>
>
> with regards,
>
> -Abhishek
>
> ________________________________
> From: Dey, S. <s.dey.student.rug.nl>
> Sent: Monday, July 17, 2017 4:55:10 AM
> To: amber.ambermd.org
> Subject: [AMBER] Error in LEaP
>
> Hi,
>
> I am trying to generate topology for FAD ligand (Flavin Adenine
> Dinucleotide) using Ambertools 16.
>
> So, I generated resp charges after running Gaussian and also generated
> frcmod using parmchk. However, as I am trying to run LEaP, it is showing
> error. I am using the following code in my leap.in file:
>
> * source /usr/local/amber9/dat/leap/cmd/leaprc.gaff *
>
> * loadamberparams /usr/local/amber9/dat/leap/parm/gaff.dat*
>
> * M = loadmol2 name.mol2*
>
> * mods = loadamberparams frcmod *
>
> * saveamberparm M prmtop inpcrd*
>
> * quit*
>
>
> However, it is showing error message :
>
>
> *teLeap -f leap.in <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__leap.in_&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&m=jvb-uGD3M_V0oUYsZsUnz64n_v2_ZLQh90py4WweKtY&s=VI_
> XIuBrayA2XTkzynrApKM1iuu0BhgkVSzNnbg7YlY&e= >*
> *-f: Source leap.in <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__leap.in_&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&m=jvb-uGD3M_V0oUYsZsUnz64n_v2_ZLQh90py4WweKtY&s=VI_
> XIuBrayA2XTkzynrApKM1iuu0BhgkVSzNnbg7YlY&e= >.*
>
> *Welcome to LEaP!*
> *(no leaprc in search path)*
> *Sourcing: ./leap.in <https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__leap.in_&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&m=jvb-uGD3M_V0oUYsZsUnz64n_v2_ZLQh90py4WweKtY&s=VI_
> XIuBrayA2XTkzynrApKM1iuu0BhgkVSzNnbg7YlY&e= >*
> *ERROR: syntax error*
>
> *: not foundpen file leaprc.gaff*
> *loadAmberParams: Improper number of arguments!*
> *usage: <variable> = loadAmberParams <filename>*
> *: not foundpen file fad.mol2*
> *saveAmberParm: Argument #1 is type String must be of type: [unit]*
> *usage: saveAmberParm <unit> <topologyfile> <coordfile>*
> *ERROR: syntax error*
>
> So, can someone tell me what is the problem with this and how to solve this
> out?
>
> With regards,
> Souvik
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Received on Tue Jul 18 2017 - 08:30:03 PDT
