Hi,
I have some questions about heme-contained protein. When I dealt with this kind of protein in tleap, I used the heme parameters provided by David A Case who had added NP and NO nonbond parameters to old HEM parametrization files. Unfortunately, CX nonbond parameters have not been provided, so I can not save the top files of the heme-contained protein. My question is how and from where I can get these parametrizations.
The error obtain is written below:
>sourcing: /home/zou/amber14//dat/leap/cmd/oldff/leaprc.ff99SB
>source leaprc.gaff
>loadamberparams heme.frcmod
>loadamberprep Heme-all-atom.prep
>HEM=loadpdb HEM.pdb
> check HEM
Checking 'HEM'....
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
Warning: Close contact of 1.451512 angstroms between .R<HEM 393>.A<HGM 64> and .R<HEM 393>.A<HP74 10>
Checking parameters for unit 'HEM'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 2
Unit is OK.
> saveamberparm HEM HEM.prmtop HEM.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
For atom: .R<HEM 393>.A<CBB 32> Could not find vdW (or other) parameters for type: CX
For atom: .R<HEM 393>.A<CBC 48> Could not find vdW (or other) parameters for type: CX
Parameter file was not saved.
Thank your for your help!
Sincerely,
Allen Zou
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Received on Fri Jun 03 2016 - 02:30:02 PDT
