AMBER Archive (2004)

Subject: Re: AMBER: Using TIP4P water in free energy calculation

From: Lijiang Yang (lijiangy_at_uci.edu)
Date: Fri Aug 06 2004 - 13:42:06 CDT

Hi, Dr. Case
   I am sorry for the messy of my last post. I will post it again. But I think you have got the
most important information. By looking at my perturbation file with rdparm, there are no
regular bonds. However, I have checked perturbation topology file prmtop.pert in test/pheTI.
The same thing happened, no regular bonds but pertbonds. And I also checked bonds in LEaP,
the bonds still exist!
Following is information I collected from LEaP and rdparm:
1. LEaP Information(perturbed LEU which is solvated by TIP4P):
> desc LEU.1.5
ATOM
             Normal Perturbed
Name: CB CB
Type: CT DC
Charge: -0.1102 0.000
Polarization: 0.0000 0.000
Element: C (not affected by pert)
Atom flags: (decimal 196611 hex 0x30003)
 posfxd n posblt n posdrwn n selected Y
 pert Y notdisp n touched Y posknwn Y
 internal n needsmin n needsbuild n
Atom position: 0.424352, -0.615175, -1.426900
Atom velocity: 0.000000, 0.000000, 0.000000
  Bonded to .R<LEU 1>.A<HB2 6> by a single bond.
  Bonded to .R<LEU 1>.A<HB3 7> by a single bond.
  Bonded to .R<LEU 1>.A<CG 8> by a single bond.
  Bonded to .R<LEU 1>.A<HB1 20> by a single bond.

2. rdparm information of pheTI
RDPARM MENU: bonds :1
Mask [:1] represents 15 atoms
 
    Bond Kb Req atom names (numbers)
 
RDPARM MENU: pertbonds :1
Mask [:1] represents 15 atoms
 
   Bond
lambda Kb Req atom names (numbers)
0 1: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 1: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 2: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 2: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 3: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 3: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 4: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 4: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 5: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 5: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 6: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 6: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 7: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 7: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 8: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 8: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 9: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 9: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 10: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 10: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 11: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 11: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 12: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 12: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 13: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 13: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 14: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 14: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
 
0 15: 367.00 1.080 :1_at_CB :1_at_CB (1,1)
1 15: 367.00 1.080 :1_at_CB :1_at_CB (1,1)

3. rdparm information of my LEU in TIP4P
RDPARM MENU: bonds :1
Mask [:1] represents 14 atoms
 
    Bond Kb Req atom names (numbers)

RDPARM MENU: pertbonds :1
Mask [:1] represents 14 atoms
 
   Bond
lambda Kb Req atom names (numbers)
0 1: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 1: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 2: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 2: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 3: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 3: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 4: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 4: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 5: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 5: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 6: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 6: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 7: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 7: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 8: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 8: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 9: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 9: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 10: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 10: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 11: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 11: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 12: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 12: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
 
0 13: 553.00 0.150 :1_at_CB :1_at_CB (1,1)
1 13: 553.00 0.150 :1_at_CB :1_at_CB (1,1)

4. rdparm information of my LEU in TIP3P

----- Original RDPARM MENU: bonds :1
Mask [:1] represents 14 atoms
 
    Bond Kb Req atom names (numbers)
RDPARM MENU: pertbonds :1
Mask [:1] represents 14 atoms
 
   Bond
lambda Kb Req atom names (numbers)
0 1: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 1: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 2: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 2: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 3: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 3: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 4: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 4: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 5: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 5: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 6: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 6: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 7: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 7: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 8: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 8: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 9: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 9: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 10: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 10: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 11: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 11: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 12: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 12: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
 
0 13: 0.00 0.000 :1_at_CB :1_at_CB (1,1)
1 13: 0.00 0.000 :1_at_CB :1_at_CB (1,1)

Thank you.

Lijiang Yang

Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Friday, August 06, 2004 8:56 AM
Subject: Re: AMBER: Using TIP4P water in free energy calculation

> It is very hard to follow what you are posting (maybe your mail program is
> mangling the output), but it looks like you have no bonds present in residue
> 1. This would explain why the atoms fly apart. If you edit your residue
> in xleap, you should see the bonds (if they are there). The "desc" command
> in LEaP can also give you information about bonds. You need to try to figure
> out what you did to end up with a residue with no bonds. Try making an
> ordinary (nonpert) prmtop file corresponding to the lambda=0 state, and see
> if you can get that to work.
>
> You seem to have pertbonds but no regular bonds.
>
> ...good luck...dac
 
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