If you search the amber list archives or the web generally for one of
the Warnings and one of the FATALs, you'll likely find more clues than I
can give at the moment.
Bill
On 9/20/19 2:18 AM, 2018808152.njau.edu.cn wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 20 2019 - 03:00:01 PDT
