I generated the BarnaseBarstar.mdcrd file by hand. I am essentially generating structures with different orientations of Barnase relative to Barstar and using sander to calculate the potential energy of their interaction. We have actually decided to go in a different direction with that and use a different program.
-Aaron
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Saturday, August 10, 2013 5:09 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Trajectory post-processing
Hi,
I received your files, and there are a few problems with them. There
is a close contact in 'BaranseBarstar.prmcrd':
CHECKSTRUCTURE: Checking atoms in mask [*].
Checking inter-atom and bond distances.
Warnings will be printed for bond lengths > eq + 1.15 Ang
and non-bond distances < 0.80 Ang.
CHECKSTRUCTURE: * (3103 atoms, 3137 bonds), imaging off.
100% Complete.
1 Warning: Atoms 565:LYS_37.HB3 and 578:LYS_37.HZ3 are close (0.62)
This indicates that the structure probably requires some minimization
before running any dynamics with it. 'BaranseBarstar.mdcrd' also
contains some close contacts:
CHECKSTRUCTURE: * (3103 atoms, 3137 bonds), imaging off.
----- [BaranseBarstar.mdcrd] (1-1, 1) -----
100% Complete.
1 Warning: Atoms 522:VAL_34.N and 2211:GLY_139.O are close (0.54)
1 Warning: Atoms 526:VAL_34.CB and 2214:GLU_140.CA are close (0.46)
1 Warning: Atoms 535:VAL_34.HG23 and 2213:GLU_140.H are close (0.40)
1 Warning: Atoms 538:ALA_35.N and 2231:ASN_141.CB are close (0.58)
1 Warning: Atoms 565:LYS_37.HB3 and 578:LYS_37.HZ3 are close (0.62)
1 Warning: Atoms 569:LYS_37.CD and 2218:GLU_140.HB3 are close (0.74)
1 Warning: Atoms 573:LYS_37.HE2 and 1964:HIE_125.CB are close (0.76)
These close overlaps are probably what's causing your VDW term to
skyrocket. The 2214:GLU_140.CA atom (second warning) is the one
reported in the post-process output for GMAX:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.3468E+10 4.9682E+09 2.1026E+11 CA 2214
GMAX is very useful in general for tracking down structural problems.
By the way, I'm not sure how you generated the 'BaranseBarstar.mdcrd'
trajectory file you gave me, but it was corrupted (file had no EOL). I
was able to fix it by re-saving the file. Out of curiosity, did you
use ptraj/cpptraj to generate it?
-Dan
On Fri, Aug 9, 2013 at 9:28 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Could you send me off-list the topology, input coordinates, and 1
> frame of the trajectory in question so I can reproduce on this end?
> Thanks.
>
> -Dan
>
> On Thu, Aug 8, 2013 at 10:48 AM, VanDyne_Aaron
> <VanDyne_Aaron.roberts.edu> wrote:
>> I ran the check command, and no bad overlaps were found. The trajectory has the same coordinates as the .prmcrd file, which gives a realistic number when used with the default imin.
>>
>> -Aaron van Dyne
>> ________________________________________
>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> Sent: Thursday, August 08, 2013 11:27 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Trajectory post-processing
>>
>> Hi,
>>
>> On Thu, Aug 8, 2013 at 8:39 AM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu> wrote:
>>> AMBER has now been updated on the supercomputer, but I am still having the same problem.
>>
>> Did you ever run the 'check' command in cpptraj/ptraj to look for bad
>> overlaps in the trajectory that is giving you the large VDW energy?
>>
>>> On Tue, Aug 6, 2013 at 2:50 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu> wrote:
>>>> The outputted energies always have a van der Waals contribution that is on the order of 10^16.
>>
>>> This indicates you have a clash somewhere in your trajectory file. Use
>>> the 'check' command in cpptraj or ptraj to see if there are any bad
>>> overlaps.
>>
>> -Dan
>>
>>>
>>> -Aaron van Dyne
>>> ________________________________________
>>> From: Jason Swails [jason.swails.gmail.com]
>>> Sent: Tuesday, August 06, 2013 8:13 PM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] Trajectory post-processing
>>>
>>> On Tue, Aug 6, 2013 at 5:59 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu>wrote:
>>>
>>>> I am using Amber 12. I do not know which bug fixes have been applied (I am
>>>> running on the University of Pittsburgh Department of Computational and
>>>> Systems Biology computing cluster. I would imagine all the appropriate bug
>>>> fixes have been applied).
>>>>
>>>
>>> You can find out with the command
>>>
>>> $AMBERHOME/update_amber --version
>>>
>>> The assumption that supercomputers keep their installations up-to-date is
>>> rarely a good one. Since they are not regular users, they probably update
>>> only when requested.
>>>
>>> You can use the command:
>>>
>>> $AMBERHOME/update_amber --check
>>>
>>> to see if there are available updates.
>>>
>>> HTH,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> BioMaPS,
>>> Rutgers University
>>> Postdoctoral Researcher
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Aug 10 2013 - 18:00:08 PDT
