Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory

From: wliu <wliu.itcs.ecnu.edu.cn>
Date: Wed, 03 Sep 2014 17:58:57 +0800

Hi,again

   I think I met another problem about my topology file. I have tried
Dan's
suggestion, and I use cpptraj to get the amber topology file named
amber.prmtop:

parm chamber22gro.prmtop
parmwrite out amber.prmtop nochamber

And I want to test if these two topology files give the same energy
result
while calculating one step and the same structure's energy. I use one
rst file but I get
two different energy terms especially for 1-4NB:

chamber prmtop file output:
  NSTEP = 0 TIME(PS) = 4425.800 TEMP(K) = 450.19 PRESS =
    0.0
  Etot = -23837.0829 EKtot = 9030.7484 EPtot =
-32867.8313
  BOND = 35.5658 ANGLE = 64.1482 DIHED =
48.7545
  UB = 8.6678 IMP = 5.6328 CMAP =
-11.0822
  1-4 NB = 58.9498 1-4 EEL = 641.6152 VDWAALS =
3169.0844
  EELEC = -36889.1674 EHBOND = 0.0000 RESTRAINT =
0.0000
  Ewald error estimate: 0.1193E-04
-------------------------------------------------------------------------------------------
amber prmtop file output:
  NSTEP = 0 TIME(PS) = 4425.800 TEMP(K) = 450.19 PRESS =
    0.0
  Etot = -23759.2938 EKtot = 9030.7484 EPtot =
-32790.0421
  BOND = 35.5658 ANGLE = 64.1482 DIHED =
48.7545
  1-4 NB = 139.9570 1-4 EEL = 641.6152 VDWAALS =
3169.0844
  EELEC = -36889.1672 EHBOND = 0.0000 RESTRAINT =
0.0000
  Ewald error estimate: 0.1193E-04

So as you will see, their 1-4NB energy have the difference value of 81
kcal/mol. This value
is quite large so I have no idea which prmtop file should be chosen to
run my MD simulation
and why their results have such a big difference?
I packed my results as appendix, hoping helpful.

hope for reply!Thanks a lot~~

Wei Liu

On 2014-09-02 22:08, wliu wrote:
> Hi, Dan
>
> Thank you for your reply and solutions! I will try your
> suggestions!
>
> Wei Liu
>
> On 2014-09-02 21:59, Daniel Roe wrote:
>> Hi,
>>
>> CPPTRAJ currently won't recognize these trajectories. A fix is in
>> progress. In the meantime, you may be able to temporarily get around
>> this by changing the first 4 characters of your trajectory file from
>> 'RXSG' to 'REMD' and using the remdtraj/remdtrajtemp keywords in
>> place
>> of rxsgldtraj/rxsgldid, as I believe all of the trajectory
>> processing
>> functionality is otherwise the same.
>>
>> Alternatively, you could use cpptraj or parmed to convert your
>> CHAMBER topology to an Amber one suitable for trajectory processing
>> with ptraj. For cpptraj this is just:
>>
>> parm chamber22gro.prmtop
>> parmwrite out myparm.parm7 nochamber
>>
>> Hope this helps, and thanks for the report.
>>
>> -Dan
>>
>> On Tue, Sep 2, 2014 at 7:40 AM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
>>> Hi,Jason
>>>
>>> I try CPPTRAJ just now, but it says that:
>>>
>>> CPPTRAJ: Trajectory Analysis. V14.00
>>> ___ ___ ___ ___
>>> | \/ | \/ | \/ |
>>> _|_/\_|_/\_|_/\_|_
>>> Reading '../step5/chamber22gro.prmtop' as Amber Topology
>>> CHAMBER topology: 1: CHARMM 31 * CHARMM22STAR
>>> CHARMM22STAR
>>> CHARMM22STAR CHARMM22STAR CHARMM
>>> INPUT: Reading Input from STDIN
>>> [trajin ../step5/crd/rxsg25.mdcrd.001 rxsgldtraj rxsgldid 1]
>>> Error: Could not determine trajectory ../step5/crd/rxsg25.mdcrd.001
>>> format.
>>> Error: Could not set up input trajectory
>>> '../step5/crd/rxsg25.mdcrd.001'.
>>> 1 errors encountered reading input.
>>> TIME: Total execution time: 0.0883 seconds.
>>>
>>> Need your help!
>>>
>>> Wei Liu
>>>
>>> On 2014-09-02 21:27, Jason Swails wrote:
>>>> On Tue, Sep 2, 2014 at 9:05 AM, wliu <wliu.itcs.ecnu.edu.cn>
>>>> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> Recently I use CHAMBER program transformed CHARMM parameter
>>>>> file
>>>>> to
>>>>> AMBER prmtop file and run a replica exchanging self-guided (RXSG)
>>>>> MD. I
>>>>> met the problem when I use ptraj to extract the RXSG MD
>>>>> trajectory.
>>>>> The
>>>>> error information was shown as follows:
>>>>>
>>>>> WARNING in scanDouble: ...scanning chrg
>>>>>
>>>>> Residue labels:
>>>>>
>>>>> TYR TYR ASP PRO GLU THR GLY THR TRP TYR
>>>>> SOD SOD WAT WAT WAT WAT WAT WAT WAT WAT
>>>>> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
>>>>> ...
>>>>> WAT WAT WAT WAT WAT
>>>>>
>>>>> There were errors upon reading parm file!!!
>>>>>
>>>>> PTRAJ: Processing input from "STDIN" ...
>>>>>
>>>>> PTRAJ: trajin ../step5/crd/rxsg25.mdcrd.001 rxsgldtraj rxsgldid 1
>>>>> Checking coordinates: ../step5/crd/rxsg25.mdcrd.001
>>>>>
>>>>> It seems that ptraj can't recognize my parm file. So I also
>>>>> update
>>>>> Amber12 to do some patching, but still have the same problem. I
>>>>> know
>>>>> that the parm file from CHARMM force field using CHAMBER may have
>>>>> some
>>>>> differences from AMBER parm on format like %FLAG CHARGE:
>>>>> charmm to amber parm file:
>>>>> %FORMAT(3e24.16)
>>>>> -0.5466849549786422E+01 0.6013534504765064E+01
>>>>> 0.6013534504765064E+01
>>>>> 0.6013534504765064E+01 0.3826794684850495E+01
>>>>> 0.1822283183262141E+01
>>>>> -0.3280109729871853E+01 0.1640054864935927E+01
>>>>> 0.1640054864935927E+01
>>>>> but amber parm file:
>>>>> %FLAG CHARGE
>>>>> %FORMAT(5E16.8)
>>>>> 3.36930327E+00 3.45859254E+00 3.45859254E+00 3.45859254E+00
>>>>> 1.03320441E+00
>>>>> 1.42498386E+00 4.73050908E+00 4.97468790E-01 4.97468790E-01
>>>>> -1.22344522E+01
>>>>> and charmm to amber file seems to have no %FLAG BOX_DIMENSIONS
>>>>> information in parm file. But I have already run the simulation
>>>>> using
>>>>> this parm file successfully. So I think this parm file is ok.
>>>>> I have no idea about this error. I wonder how to solve the
>>>>> problem
>>>>> and why ptraj can't read my parm file?
>>>>>
>>>>
>>>> Use cpptraj instead. cpptraj understands chamber topology files.
>>>>
>>>> HTH,
>>>> Jason
>>>>
>>>
>>> _______________________________________________
>>> 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 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber



Received on Wed Sep 03 2014 - 03:30:02 PDT
Custom Search