AMBER Archive (2009)

Subject: [AMBER] RE: the copper paramter

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 20 2009 - 16:38:14 CDT

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_at_gmail.com]
Sent: Monday, July 20, 2009 2:11 PM
To: amber_tutorial_query_at_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

 

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber