Dear Amber developers:Some trouble bothered me when I simulated my protein and ligand with amber following amber tutorial 'Using Antechamber to Create LEaP Input Files for Simulating Sustiva (efavirenz)-RT complex
using the General Amber Force Field' .I successfully created ligand's lib file,inprcd file and prmtop file.Then I tried to created complex's inprcd and prmtop file.
tleap -f oldff/leaprc.ff99SB
> source leaprc.gaff
> loadamberparams DBP.frcmod
> loadoff sus.lib
> complex = loadpdb EstJ6_DBP_bound_sus.pdb
These above steps are correct.When I type the following commmand :
> saveamberparm complex EstJ6_DBP_bound_sus.prmtop EstJ6_DBP_bound_sus.inpcrd
some problems had arisen:
Warning: There is a bond of 5.004838 angstroms between:
Warning: There is a bond of 7.294518 angstroms between:
Warning: There is a bond of 5.021115 angstroms between:
Warning: There is a bond of 6.477685 angstroms between:
Warning: There is a bond of 5.753477 angstroms between:
Warning: There is a bond of 5.831261 angstroms between:
Warning: There is a bond of 8.305426 angstroms between:
Warning: There is a bond of 5.831089 angstroms between:
Warning: There is a bond of 6.082968 angstroms between:
Warning: There is a bond of 8.116871 angstroms between:
Warning: There is a bond of 9.057616 angstroms between:
Warning: There is a bond of 6.801059 angstroms between:
Warning: There is a bond of 3.132092 angstroms between:
Warning: There is a bond of 4.543127 angstroms between:
Warning: The unperturbed charge of the unit (-3.001000) is not zero.
FATAL: Atom .R<HIE 76>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 88>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 114>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 139>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 223>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 270>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 273>.A<HD1 18> does not have a type.
Error: Failed to generate parameters
Could you give me some suggestions?I'm looking forward to your reply.
Sincerely yours,
Jiarong Qiu
Nanjing Agricultural University
Ph.D. Graduate Student
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Received on Fri Sep 20 2019 - 02:30:02 PDT
