AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Nov 14 2008 - 15:00:30 CST

file formats are on the amber web site.
when you're debugging, always run single cpu if you have problems.
often error messages on non-master nodes do not go to the output file,
since only the master has access.

On Fri, Nov 14, 2008 at 3:55 PM, Chin, Keith B
<keith.b.chin_at_jpl.nasa.gov> wrote:
> 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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