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 Mon Jul 17 2017 - 09:30:03 PDT
