Hi John,
Please post such questions to the AMBER mailing list in future. This is the
best place for them. See
http://lists.ambermd.org/ for signup details.
>From what you show below I cannot see where you are loading the frcmod file.
The CUA.lib file just defines the topology, not the parameters. It explains
this in the tutorial and then in section 4 gives you a frcmod file (with
completely fictional parameters) to try.
All the best
Ross
From: Jianzhong(John) Liu [mailto:liujzus.gmail.com]
Sent: Monday, July 20, 2009 2:11 PM
To: amber_tutorial_query.rosswalker.co.uk
Subject: the copper paramter
Hello, Ross,
Why I use the tutorial to run copper parameter in your website still said
cannot find copper parameters?
http://ambermd.org/tutorials/advanced/tutorial1_orig/section3.htm
I used the same CUA.lib file you put on web. Following is my leap log file.
> loadoff cua.lib
Loading library: ./cua.lib
Loading: CUA
> 1PLC = loadpdb plc.pdb
Loading PDB file: ./plc.pdb
.
.
.
> bond 1PLC.37.ND1 1PLC.100.CU
> bond 1PLC.87.ND1 1PLC.100.CU
> bond 1PLC.84.SG 1PLC.100.CU
> bond 1PLC.92.SD 1PLC.100.CU
> solvateoct 1PLC TIP3PBOX 12
(using default radius 1.500000 for CU)
Scaling up box by a factor of 1.289865 to meet diagonal cut criterion
Solute vdw bounding box: 32.290 40.847 34.364
.
.
.
> addions 1PLC Na+ 9
Adding 9 counter ions to "1PLC" using 1A grid
Used default radius 1.50 for 1 atoms
Total solute charge: -9.00 Max atom radius: 2.00
.
.
.
> saveamberparm 1PLC 1PLC.prmtop 1PLC.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<CUA 100>.A<CU 1> Could not find type: CU
Parameter file was not saved.
Thanks,
John
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Received on Mon Jul 20 2009 - 18:09:11 PDT
