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Re: Calculation of rmsd from NAMD coor file judkil21 09/24/22 06:40 PM
The pdb files are necessarily read with an option (RESID or SEGI or CHAIN) because they are not native files. And if I don't add one of these options, charmm will write me that I am missing atoms.
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Re: Calculation of rmsd from NAMD coor file judkil21 09/24/22 06:18 PM
For bomlev -5 : In miscom, paragraph 14,

"-5,-4 Limit exceeded type of errors" this is the only line where I don't see what exceeded type of errors means.

As I'm in the learning phase, it would be a value of -1 that I should put.

In test/c39test/readpdb.inp we call directly the necessary segment when we read the pdb file, interesting
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Re: Calculation of rmsd from NAMD coor file lennart 09/24/22 02:16 PM
READ COOR PDB takes several options that make it possible to avoid splitting the file: RESI to override residue numbers and instead use RESID and SEGID information. CHAIN <chain id> or SEGI <segi> reads just the lines in the file that contain the specified CHAIN/SEGI information (which may or may not be the same as the PSF SEGI since it is just a filter applied to the reading of the PDB coordinate file). There are also options to use or skip certain lines (HETATOM, ATOM, specified residue names) or to map residue names in the file to names in PSF.

see test/c39test/readpdb.inp for examples. io.info may not be quite up-to-date on these options.
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Re: Calculation of rmsd from NAMD coor file rmv 09/23/22 08:13 PM
One thing to know is that CHARMM is not very graceful about reading PDB files; it is regarded as an import/export format only, and not a native file type. The Script Archive forum has a number of posts on the topic. Files with multiple segments usually require splitting into one file per segment.
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Re: Calculation of rmsd from NAMD coor file judkil21 09/22/22 12:00 PM
Ok, I will analyze,

Thanks for your advice.
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Re: Calculation of rmsd from NAMD coor file lennart 09/22/22 07:52 AM
Why do you use the command
"coor copy comp select heavy end"?

You should NOT use bomlev -5.

Since there are numerous messages about missing coordinates when you read dynami.1.coor you have to fix this first. This is your primary problem.
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Re: Calculation of rmsd from NAMD coor file judkil21 09/21/22 10:50 PM
the output smile
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Re: Calculation of rmsd from NAMD coor file judkil21 09/21/22 10:33 PM
I use a classical toppar file
The system is 7aeh.pdb : SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957

I use classical toppar.str file and classical toppar folder
In attach:
- r8h.str (the ligand str file)
- setup.psf (the ligand with the protein)

The first frame
- setup.pdb
The last frame
- dynami.1.coor

The script which gives me a 10^15 value for the rmsd
- calculate_rmsd_coor.inp


I added ".txt" at the end of the files to be able to send them but it must be removed
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Re: Calculation of rmsd from NAMD coor file lennart 09/21/22 06:14 PM
To be quite specific:
The important point is that all you have posted so far is essentially "it does not work". If you want help to solve your problem you have to post enough information for us to help you:

Post brief but complete input/output files
No streaming, no CHARMM variables, no bomlev -5 or the like.
In your most recent post showing some output, you only show the final error message.
What makes you think that there were no errors, or other relevant information earlier in the job? That is quite likely to be the case (why else would CHARMM complain about missing coordinates), hence the requirement for full input/output files.
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Re: Calculation of rmsd from NAMD coor file judkil21 09/21/22 05:06 PM
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Re: Calculation of rmsd from NAMD coor file rmv 09/21/22 03:57 PM
If you go through the READ BEFORE POSTING topic carefully, you will see there are some strong hints about what information to provide if you want assistance trouble-shooting a problem, and how to provide it.
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Re: Calculation of rmsd from NAMD coor file judkil21 09/21/22 12:11 PM
read rtf ...
read param ...
read psf ...

read psf card append name setup.psf
read coor pdb name setup.pdb
read coor pdb name dynami.1.coor COMP

define heavy select (segid HETE .and. .not. type h*) end ! For the ligands of the two structures that I want to align

coor orie rms sele heavy end


Prompt :

CHARMM> coor orie rms sele heavy end
SELRPN> 20 atoms have been selected out of 32599
**WARNING** ALL SELECTED COORDINATES UNDEFINED

**** WARNING **** FOR THIS OPERATION, THERE WERE 20 MISSING COORDINATES
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Re: Calculation of rmsd from NAMD coor file judkil21 09/21/22 11:47 AM
I have a system containing a ligand (an hetero molecule), a protein (containing amino acids) and a water box

I have realized a simulation of molecular dynamics

I would like to calculate the rsmd between, the coordinates of the ligand in the starting frame (setup.pdb, pdb format) and the coordinates of the ligand in the last frame (dynami.1.coor, pdb format)
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Re: Calculation of rmsd from NAMD coor file lennart 09/21/22 11:19 AM
This is an outline of what you want to do:
read rtf ...
read param ...
read psf ...
read coor pdb name setup.pdb
read coor pdb name dynami.1.coor COMP
coor orie rms sele type ca end
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Re: Calculation of rmsd from NAMD coor file judkil21 09/21/22 09:52 AM
Thanks

Indeed dynami.1.coor is a pdb coordinate file, not a binary file, I will remove the obseleted structures

That's what I want to do is to compare the rmsd of the main set with the comparison set, I tried again by adding orient protein before the rms calculation

define heavy select (segid HETE .and. .not. type h*) end
define protein sele type ca end
coor orient rms sele protein end
coor rms select heavy end
set rmsd ?rms


I obtain


CHARMM> coor orient rms select heavy end
SELRPN> 20 atoms have been selected out of 32659
**WARNING** ALL SELECTED COORDINATES UNDEFINED

**** WARNING **** FOR THIS OPERATION, THERE WERE 20 MISSING COORDINATES
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Re: Calculation of rmsd from NAMD coor file lennart 09/21/22 06:45 AM
Your statement "open read unform ....." only open the file, no reading is done.
Is dynami.1.coor a binary file? It is better to work with formatted coordinate files, either in pdb-format or the charmm format.
To avoid the confusion the obsolete construct with an open statement followe by a read or write should be avoided (open is still necessary in some cases):
read psf card append name setup.psf (I am not sure that xplor is needed)
read coor pdb name setup.pdb
read namd file dynami.1.coor

Note also that
coor copy comp select heavy end
copies coordinates from the main set (which came from setup.pdb) to the comparison set, and that the following RMS calculation is therefore performed on two identical coordinate sets.
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Re: Calculation of rmsd from NAMD coor file judkil21 09/20/22 09:24 PM
CHARMM> coor copy comp select heavy end
SELRPN> 20 atoms have been selected out of 32599
SELECTED COORDINATES COPIED TO THE COMPARISON SET.


CHARMM> coor orient rms select heavy end
SELRPN> 20 atoms have been selected out of 32599
CENTER OF ATOMS BEFORE TRANSLATION -0.73425 1.86415 0.97435
CENTER OF REFERENCE COORDINATE SET -0.73425 1.86415 0.97435
NET TRANSLATION OF ROTATED ATOMS 0.00000 0.00000 0.00000
ROTATION MATRIX
1.000000 -0.000000 -0.000000
-0.000000 1.000000 0.000000
0.000000 -0.000000 1.000000
VERY LITTLE ROTATION: NO AXIS FOUND
TOTAL SQUARE DIFF IS 0.0000 DENOMINATOR IS 20.0000
THUS RMS DIFF IS 0.000000
ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS.


CHARMM> set rmsd ?rms
RDCMND substituted energy or value "?RMS" to "2.581522112E-15"
Parameter: RMSD <- "2.581522112E-15"

CHARMM>

CHARMM> open write unit 30 card name rmsd_first-last-frames_coor.txt
VOPEN> Attempting to open::rmsd_first-last-frames_coor.txt::
OPNLGU> Unit 30 opened for WRITE access to rmsd_first-last-frames_coor.txt

CHARMM> write title unit 30
RDTITL> * 2.581522112E-15
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Re: Calculation of rmsd from NAMD coor file judkil21 09/20/22 09:17 PM
In setup.pdb and dynami.1.coor there are : a protein, a ligand in a water box.

I made a simulation setup.pdb is the first frame and dynami.1.coor is the last frame.

The value of rmsd should be between 0 and 3. Here is the value I get 2.581522112E-15

From my readings, Charmm works with main set and comp set but it still doesn't work
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Re: Calculation of rmsd from NAMD coor file lennart 09/20/22 03:12 PM
As far as I can tell you did not actually read more than one coordinate set. So getting the rmsd between two identical coordinate sets is indeed expected to return zero, within numerical (double) precision.
And I hope you understand that BOMLEV -5 is an absolute No-No if you want to get help ....
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Re: Calculation of rmsd from NAMD coor file rmv 09/19/22 06:27 PM
From the CHARMM documentation, it appears that the command to read a NAMD file may be

READ NAMD FILE "filename"
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Calculation of rmsd from NAMD coor file judkil21 09/19/22 02:02 PM
Hello, I try to calculate rmds between a pdb file and NAMD coor file.

Code
bomlev -5
wrnlev  5

stream toppar.str
stream job.str

open unit 10 read card name setup.psf
read psf xplor card unit 10 append

open unit 10 read card name setup.pdb
read coord pdb unit 10

open read unform unit 22 name dynami.1.coor

define heavy select (segid HETE .and. .not. type h*) end
 
coor copy comp select heavy end
 
coor orient rms select heavy end

set rmsd ?rms

    
open write unit 30 card name rmsd_first-last-frames_coor.txt
write title unit 30
* @rmsd

stop


I obtain value like 1.310232404E-15

Does anyone know where the error is?
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