AMBER Archive (2008)

Subject: RE: AMBER: Sander *.top and *.crd file from PDB file

From: Chin, Keith B (keith.b.chin_at_jpl.nasa.gov)
Date: Fri Nov 14 2008 - 14:55:57 CST

1. Does sander pass all the test cases?

Yes. My installation was successful, meaning all test cases passed

2. What actually is in the output file?

The output file contains only Amber header with no computational results listed after 5 minutes.

3. What actually is your input file?

I'm not sure, but this same input file worked on liquid water simulation using tip4p *.top and *.crd provided in tip4p directory from installation package.

What specifically makes you think it is a prmtop or box size issue?

I did not specify any box dimensions in my pdb file, thus, not sure how xleap SaveAmberParm cmd generate *top and *crd PBC parameters for sander to recognize. Here's a glimpse of my ice pdb file format from beginning to 9th molecule:

ATOM 1 O TP4 1 2.258 1.304 6.891 0.000
ATOM 2 H1 TP4 1 2.258 1.304 5.891 0.417
ATOM 3 H2 TP4 1 3.083 1.780 7.220 0.417
ATOM 4 EPW TP4 1 2.363 1.364 6.804 -0.834
TER
ATOM 5 O TP4 2 2.258 1.304 14.245 0.000
ATOM 6 H1 TP4 2 2.258 1.304 13.245 0.417
ATOM 7 H2 TP4 2 3.083 1.780 14.574 0.417
ATOM 8 EPW TP4 2 2.363 1.364 14.158 -0.834
TER
ATOM 9 O TP4 3 2.258 1.304 21.599 0.000
ATOM 10 H1 TP4 3 2.258 1.304 20.599 0.417
ATOM 11 H2 TP4 3 3.083 1.780 21.928 0.417
ATOM 12 EPW TP4 3 2.363 1.364 21.512 -0.834
TER
ATOM 13 O TP4 4 0.000 5.215 6.891 0.000
ATOM 14 H1 TP4 4 0.000 5.215 5.891 0.417
ATOM 15 H2 TP4 4 0.825 5.691 7.220 0.417
ATOM 16 EPW TP4 4 0.105 5.275 6.804 -0.834
TER
ATOM 17 O TP4 5 0.000 5.215 14.245 0.000
ATOM 18 H1 TP4 5 0.000 5.215 13.245 0.417
ATOM 19 H2 TP4 5 0.825 5.691 14.574 0.417
ATOM 20 EPW TP4 5 0.105 5.275 14.158 -0.834
TER
ATOM 21 O TP4 6 0.000 5.215 21.599 0.000
ATOM 22 H1 TP4 6 0.000 5.215 20.599 0.417
ATOM 23 H2 TP4 6 0.825 5.691 21.928 0.417
ATOM 24 EPW TP4 6 0.105 5.275 21.512 -0.834
TER
ATOM 25 O TP4 7 -2.258 9.126 6.891 0.000
ATOM 26 H1 TP4 7 -2.258 9.126 5.891 0.417
ATOM 27 H2 TP4 7 -1.433 9.602 7.220 0.417
ATOM 28 EPW TP4 7 -2.153 9.186 6.804 -0.834
TER
ATOM 29 O TP4 8 -2.258 9.126 14.245 0.000
ATOM 30 H1 TP4 8 -2.258 9.126 13.245 0.417
ATOM 31 H2 TP4 8 -1.433 9.602 14.574 0.417
ATOM 32 EPW TP4 8 -2.153 9.186 14.158 -0.834
TER
ATOM 33 O TP4 9 -2.258 9.126 21.599 0.000
ATOM 34 H1 TP4 9 -2.258 9.126 20.599 0.417
ATOM 35 H2 TP4 9 -1.433 9.602 21.928 0.417
ATOM 36 EPW TP4 9 -2.153 9.186 21.512 -0.834
TER

Is there more detailed info on file formats, specifically *top and *crd files, for sander in case I want to produce these files independent of leap?

Hope this helps.

Thanks.

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Gustavo Seabra
Sent: Friday, November 14, 2008 12:30 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Sander *.top and *.crd file from PDB file

On Fri, Nov 14, 2008 at 2:43 PM, Chin, Keith B wrote:

> Hi,

> I'm using Amber9 in an attempt to simulate bulk and surface ice.

>

> I created a pdb file of ice lattice containing 216 TIP4P water molecules

> which successfully loads in xleap. From xleap, I was able to generate *.top

> and *.crd files for min and md simulations using sander.

>

> Problem: During sander min run, the run just stays active BUT produced no

> results. My min.out file contains only the Amber header after I terminated

> the run using Cntl + C unix command.

>

> I interpret this as an *.top issue. I'm not sure if I set my periodic

> boundary conditions correctly for 216 water molecule in ice lattice. My

> lattice dimensions for this ice lattice are: x= 13.548A, y= 27.096A, y=

> 22.062, alpha = 90, beta=90, and gamma = 120.

>

> Does xleap automatically recognize these dimensions from my pdb file for do

> I have to set it manually as well? If so, do I use xleap or ptraj for this

> process?

>

> Any advise would be greatly appreciated.

You will need to give us more information here.

1. Does sander pass all the test cases?

2. What actually is in the output file?

3. What actually is your input file?

What specifically makes you think it is a prmtop or box size issue? 

--

Gustavo Seabra

Postdoctoral Associate

Quantum Theory Project - University of Florida

Gainesville - Florida - USA

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