I figured out that the frcmod.NAD file was loaded incorrectly. I corrected this error and that solved the problem. Thank you for the mailing list which has lots of information.
Thanks and regards,
Latha.
From: Prema Mallipeddi
Sent: Friday, January 24, 2014 3:43 PM
To: 'amber.ambermd.org'
Subject: Error generating prmtop file for protein with NAD+
I have to simulate a protein with NAD+. I obtained NAD+.lib file and and frc.NAD+ file from
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
I changed the atomnames in pdb file to those in NAD+.lib file.
I then applied the following commands
1) tleap -f leaprc.ff99SB
2) source leaprc.gaff
3) loadamberparams frcmod.NAD+
4) loadoff NAD+.lib
5) complex = loadpdb prot_nad.pdb
6) saveamberparm complex prot_nad.prmtop prot_nad.inpcrd
I got the following error for the last few atoms of NAD+. The program seem to have no problem with the first few lines of NAD+. To crosscheck, I converted the NAD+.lib to pdb and repeated same step. I end up with same error.
For atom: .R<NDP 266>.A<N6 36> Could not find vdW (or other) parameters for type: NF
For atom: .R<NDP 266>.A<C16 37> Could not find vdW (or other) parameters for type: CJ
For atom: .R<NDP 266>.A<C17 38> Could not find vdW (or other) parameters for type: CF
For atom: .R<NDP 266>.A<C18 39> Could not find vdW (or other) parameters for type: CE
For atom: .R<NDP 266>.A<O14 40> Could not find vdW (or other) parameters for type: OE
For atom: .R<NDP 266>.A<N7 41> Could not find vdW (or other) parameters for type: NE
For atom: .R<NDP 266>.A<C19 42> Could not find vdW (or other) parameters for type: CI
For atom: .R<NDP 266>.A<C20 43> Could not find vdW (or other) parameters for type: CF
For atom: .R<NDP 266>.A<C21 44> Could not find vdW (or other) parameters for type: CJ
For atom: .R<NDP 266>.A<H92 65> Could not find vdW (or other) parameters for type: HI
For atom: .R<NDP 266>.A<H86 66> Could not find vdW (or other) parameters for type: HE
For atom: .R<NDP 266>.A<H87 67> Could not find vdW (or other) parameters for type: HE
For atom: .R<NDP 266>.A<H90 68> Could not find vdW (or other) parameters for type: HI
For atom: .R<NDP 266>.A<H89 69> Could not find vdW (or other) parameters for type: HI
For atom: .R<NDP 266>.A<H81 70> Could not find vdW (or other) parameters for type: HI
Any suggestion/help in this regard is appreciated.
Thanks and regards,
Latha.
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Received on Mon Jan 27 2014 - 11:30:02 PST
