AMBER Archive (2009)

Subject: [AMBER] errors when add ions

From: zgong.hust (zgong.hust_at_gmail.com)
Date: Wed May 20 2009 - 21:51:48 CDT

Hi all:
      I would like to add magnesium to the RNA molecule before perform the MD simulations, However, when I use the tleap to add magnesium ions, some error happened
the software vision is AMBER 9, and the force filed is leaprc.rna.ff98

Here is the command

model=loadpdb xxx.pdb
addions MG2 30
solvatebox model TIP3PBOX 8.0

when I want to save the prmtop and inpcrd files, some error happened

For atom: .R<MG2 84>.A<MG 1> Could not find type: MG
For atom: .R<MG2 85>.A<MG 1> Could not find type: MG
For atom: .R<MG2 86>.A<MG 1> Could not find type: MG
For atom: .R<MG2 87>.A<MG 1> Could not find type: MG
For atom: .R<MG2 88>.A<MG 1> Could not find type: MG
For atom: .R<MG2 89>.A<MG 1> Could not find type: MG
For atom: .R<MG2 90>.A<MG 1> Could not find type: MG
For atom: .R<MG2 91>.A<MG 1> Could not find type: MG
For atom: .R<MG2 92>.A<MG 1> Could not find type: MG
For atom: .R<MG2 93>.A<MG 1> Could not find type: MG
For atom: .R<MG2 94>.A<MG 1> Could not find type: MG
For atom: .R<MG2 95>.A<MG 1> Could not find type: MG
For atom: .R<MG2 96>.A<MG 1> Could not find type: MG
For atom: .R<MG2 97>.A<MG 1> Could not find type: MG
For atom: .R<MG2 98>.A<MG 1> Could not find type: MG
For atom: .R<MG2 99>.A<MG 1> Could not find type: MG
For atom: .R<MG2 100>.A<MG 1> Could not find type: MG
For atom: .R<MG2 101>.A<MG 1> Could not find type: MG
For atom: .R<MG2 102>.A<MG 1> Could not find type: MG
For atom: .R<MG2 103>.A<MG 1> Could not find type: MG
For atom: .R<MG2 104>.A<MG 1> Could not find type: MG
For atom: .R<MG2 105>.A<MG 1> Could not find type: MG
For atom: .R<MG2 106>.A<MG 1> Could not find type: MG
For atom: .R<MG2 107>.A<MG 1> Could not find type: MG
For atom: .R<MG2 108>.A<MG 1> Could not find type: MG
For atom: .R<MG2 109>.A<MG 1> Could not find type: MG
For atom: .R<MG2 110>.A<MG 1> Could not find type: MG
For atom: .R<MG2 111>.A<MG 1> Could not find type: MG
For atom: .R<MG2 112>.A<MG 1> Could not find type: MG
For atom: .R<MG2 113>.A<MG 1> Could not find type: MG
For atom: .R<MG2 114>.A<MG 1> Could not find type: MG
For atom: .R<MG2 115>.A<MG 1> Could not find type: MG
For atom: .R<MG2 116>.A<MG 1> Could not find type: MG
For atom: .R<MG2 117>.A<MG 1> Could not find type: MG
For atom: .R<MG2 118>.A<MG 1> Could not find type: MG
Parameter file was not saved.

How can I fix this problem?

Thanks for your help

2009-05-21

Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber