AMBER Archive (2006)

Subject: Re: AMBER: RMSd error

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Fri May 26 2006 - 08:30:57 CDT

Ok THANK YOU!!!!!

claire
----- Original Message -----
From: "Carlos Simmerling" <carlos_at_csb.sunysb.edu>
To: <amber_at_scripps.edu>
Sent: Friday, May 26, 2006 2:58 PM
Subject: Re: AMBER: RMSd error

> Claire,
> let's separate the issue of time from frames.
> how often did you write the frames? Is 3598 frames correct?
> ptraj doesn't know how often you are writing since that
> info is not in the trajectory file. If the # of frames is correct
> but it is just a problem with the X values ("time") then you
> can use the time keyword. It's described in the Amber manual
> under the ptraj rms command.
> carlos
>
> Claire Zerafa wrote:
>
>> Dear Dr Simmerling
>>
>> Thanks for replying...
>>
>> Ptraj output, as seen at the VERY bottom of this email where the ptraj
>> output file is pasted, reads 3598 frames, and says it does so
>> successfully at the end of the output file. When I added the sets
>> processed in every mdcrd file, the total adds up to this 3598. I am
>> doing this for the first time, but I am under the impression that when
>> ptraj dumps the RMSd vs time data, I should see 1820ps in total which I
>> do not. Perhaps this is where I am making the mistake and all is well??
>>
>> Coordinate processing will occur on 3598 frames
>> PTRAJ: Successfully read in 3598 sets and processed 3598 sets.
>> Dumping accumulated results (if any)
>>
>> PTRAJ RMS: dumping RMSd vs time data
>>
>> Thanks again
>>
>> claire
>>
>>
>> ----- Original Message ----- From: "Carlos Simmerling"
>> <carlos_at_csb.sunysb.edu>
>> To: <amber_at_scripps.edu>
>> Sent: Friday, May 26, 2006 1:27 PM
>> Subject: Re: AMBER: RMSd error
>>
>>
>>> it would help if you replied to the last mail I posted about
>>> this. tell us how many FRAMES you have, not how many ps.
>>> I can't really understand what's going wrong unless you are
>>> very specific. are you saying that ptraj tells you it is writing
>>> 3598 values but the file does not have 3598 values?
>>> did you try removing the old rmsd output and rerunning ptraj?
>>> is there sufficient disk space available? are you using quotas?
>>>
>>> Claire Zerafa wrote:
>>>
>>>> Hi All,,
>>>> >
>>>> > I am still trying to figure out why I do not produce PMSd data for
>>>> the entire trajectory that I am reading in ptraj. I am enclosing the
>>>> output file from ptraj below. I still cannot identify any errors. It
>>>> seems that all sets were read in, and
>>>> > that the output file was generated correctly. Just I get RMSd
>>>> valvues for 719ps out or a total of 1820ps I simulated. Can anyone pick
>>>> up what I am missing please?
>>>> >
>>>> > Thanks
>>>> >
>>>> > Claire
>>>> >
>>>> > Amber8 Module: ptraj
>>>> >
>>>> > CYX GLN PRO ILE PHE LEU ASN VAL LEU GLU
>>>> > ALA ILE GLU PRO GLY VAL VAL CYS ALA GLY
>>>> > HIE ASP ASN ASN GLN PRO ASP SER PHE ALA
>>>> > ALA LEU LEU SER SER LEU ASN GLU LEU GLY
>>>> > GLU ARG GLN LEU VAL HIE VAL VAL LYS TRP
>>>> > ALA LYS ALA LEU PRO GLY PHE ARG ASN LEU
>>>> > HIE VAL ASP ASP GLN MET ALA VAL ILE GLN
>>>> > TYR SER TRP MET GLY LEU MET VAL PHE ALA
>>>> > MET GLY TRP ARG SER PHE THR ASN VAL ASN
>>>> > SER ARG MET LEU TYR PHE ALA PRO ASP LEU
>>>> > VAL PHE ASN GLU TYR ARG MET HIE LYS SER
>>>> > ARG MET TYR SER GLN CYS VAL ARG MET ARG
>>>> > HIE LEU SER GLN GLU PHE GLY TRP LEU GLN
>>>> > ILE THR PRO GLN GLU PHE LEU CYS MET LYS
>>>> > ALA LEU LEU LEU PHE SER ILE ILE PRO VAL
>>>> > ASP GLY LEU LYS ASN GLN LYS PHE PHE ASP
>>>> > GLU LEU ARG MET ASN TYR ILE LYS GLU LEU
>>>> > ASP ARG ILE ILE ALA CYX LYS ARG LYS ASN
>>>> > PRO THR SER CYS SER ARG ARG PHE TYR GLN
>>>> > LEU THR LYS LEU LEU ASP SER VAL GLN PRO
>>>> > ILE ALA ARG GLU LEU HIE GLN PHE THR PHE
>>>> > ASP LEU LEU ILE LYS SER HIE MET VAL SER
>>>> > VAL ASP PHE PRO GLU MET MET ALA GLU ILE
>>>> > ILE SER VAL GLN VAL PRO LYS ILE LEU SER
>>>> > GLY LYS VAL LYS PRO ILE TYR PHE HIE THR
>>>> > BEN WAT WAT WAT WAT WAT WAT WAT WAT WAT
>>>> > WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
>>>> > ...
>>>> > WAT
>>>> > Scanning Box
>>>> > Successfully completed readParm.
>>>> >
>>>> > PTRAJ: Processing input file...
>>>> > Input is from standard input
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdrcd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdrcd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz
>>>> >
>>>> > PTRAJ: trajin
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_10.mdrcd.gz
>>>> >
>>>> > PTRAJ: rms first out
>>>> > /DATA/VINCLOZOLIN_TRAJECTORY_ANALYSIS/vinclozolin_backbone.rms @CA
>>>> time 0.2
>>>> > Mask [@CA] represents 250 atoms
>>>> >
>>>> > PTRAJ: strip :WAT
>>>> > Mask [:WAT] represents 21090 atoms
>>>> > FYI: No output trajectory specified (trajout), none will be saved.
>>>> >
>>>> > PTRAJ: Successfully read the input file.
>>>> > Coordinate processing will occur on 3598 frames.
>>>> > Summary of I/O and actions follows:
>>>> >
>>>> > INPUT COORDINATE FILES
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz) is
>>>> > an AMBER trajectory (with box info) with 398 sets
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz) is
>>>> > an AMBER trajectory (with box info) with 400 sets
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz) is
>>>> > an AMBER trajectory (with box info) with 400 sets
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz) is
>>>> > an AMBER trajectory (with box info) with 400 sets
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdrcd.gz) is
>>>> > an AMBER trajectory (with box info) with 400 sets
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdrcd.gz) is
>>>> > an AMBER trajectory (with box info) with 400 sets
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz) is
>>>> > an AMBER trajectory (with box info) with 400 sets
>>>> > File
>>>> >
>>>> (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz) is
>>>> > an AMBER trajectory (with box info) with 400 sets
>>>> > File
>>>> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_10.mdrcd.gz)
>>>> is > an
>>>> > AMBER trajectory (with box info) with 400 sets
>>>> >
>>>> > OUTPUT COORDINATE FILE
>>>> > NULL entry
>>>> >
>>>> > ACTIONS
>>>> > 1> RMS to first frame using no mass weighting
>>>> > Dumping RMSd vs. time (with time interval 0.20) to a file named
>>>> > /DATA/VINCLOZOLIN_TRAJECTORY_ANALYSIS/vinclozolin_backbone.rms
>>>> > Atom selection follows :1-250_at_CA
>>>> > 7> STRIP: 21090 atoms will be removed from trajectory: :252-7281
>>>> >
>>>> >
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 ................................................
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdrcd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdrcd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> > Processing AMBER trajectory file
>>>> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_10.mdrcd.gz
>>>> >
>>>> > Set 1 .................................................
>>>> > Set 50 .................................................
>>>> > Set 100 .................................................
>>>> > Set 150 .................................................
>>>> > Set 200 .................................................
>>>> > Set 250 .................................................
>>>> > Set 300 .................................................
>>>> > Set 350 .................................................
>>>> > Set 400
>>>> >
>>>> > PTRAJ: Successfully read in 3598 sets and processed 3598 sets.
>>>> > Dumping accumulated results (if any)
>>>> >
>>>> > PTRAJ RMS: dumping RMSd vs time data
>>>> >
>>>
>>>
>>>
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>>
>>
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>
>
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