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have trouble reading water molecules from pdb file
#37249 12/30/18 02:58 AM
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lqz Offline OP
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Dear all:

I tried to convert a simulation system originally set up using VMD into charmm. Using charmm 40 program, I can read in the protein pdb files without any problem, but could not read in the water pdb file. I got the following error message:

...
A RESIDUE OFFSET OF 601 WILL BE USED.
INFO: A subset of total atoms will be read.

TITLE> *
At line 1626 of file /home/c40/charmm/source/io/coorio.src
Fortran runtime error: Bad value during floating point read

The following is the charmm code to read in the water coordinates from pdb file:

READ SEQU TIP3 29195
GENERATE TIP3 SETUP WARN FIRST NONE LAST NONE NOANGL NODIHE

! Read co-ordinates of tip3
! -------------------------
OPEN READ UNIT 2 CARD NAME tip3p-1.pdb
READ COOR PDB UNIT 2 APPEND
CLOSE UNIT 2


Can someone help me out? Thank you very much.

lz

Re: have trouble reading water molecules from pdb file
lqz #37250 12/30/18 03:21 AM
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rmv Offline
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In the Script Archive, see


Rick Venable
computational chemist

Re: have trouble reading water molecules from pdb file
lqz #37251 12/30/18 07:06 PM
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Hi, Rick, my pdb file is in the standard pdb format:

ATOM 1 OH2 TIP3 1 41.154 -5.264 -51.024 0.00 0.00 WT1
ATOM 2 H1 TIP3 1 41.683 -4.517 -51.303 0.00 0.00 WT1
ATOM 3 H2 TIP3 1 41.779 -5.859 -50.609 0.00 0.00 WT1
ATOM 4 OH2 TIP3 2 37.216 23.916 -58.284 0.00 0.00 WT1
ATOM 5 H1 TIP3 2 36.352 23.916 -58.696 0.00 0.00 WT1
ATOM 6 H2 TIP3 2 37.793 24.313 -58.937 0.00 0.00 WT1

I do not know why it can not be read in.

I defined univer.str with the content below based on the pdb file I posted above:

* define custom format for the water PDB files
*

read univ
* custom pdb
*
unknown
iseq 7 5
type 13 4
resn 18 4
segi 22 1
resi 23 5
x 32 8
y 40 8
z 48 8
w 62 6
!titl 1 4 CRYS
!excl 1 3 END
end

return

and read the file. Then I used the following to read the pdb file,

read sequ tip3 29195
!gener W noang nodihe
gener W setup first none last none noang nodihe
open unit 3 read card name tip3p-1.pdb
read coor univ unit 3
close unit 3
hbuild sele segid W .and. type H* end

The output showed the following error message:

***** LEVEL 1 WARNING FROM *****
***** BILDC called with a null IC table
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

I am wondering how to solve the problem. Thank you.

Re: have trouble reading water molecules from pdb file
lqz #37252 12/30/18 07:37 PM
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rmv Offline
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Based on the fragments posted, there's not a lot I can say.

Is the water SEGID W or WT1? The SEGIDs and RESIDs in any COOR files read must match the PSF.

The UNIV setup in univer.str does not appear to be correct, in that it does not match the PDB snippet posted; the SEGID is not in column 22. In some cases, that column can be the PDB chain ID, which can be used for the SEGID if present.

Your first post suggested a mismatch between water RESIDs and RESNOs may be the problem, at least for using READ COOR PDB. In principle, that should work, but may require the use of an OFFSET, as described in the "complex PDB input examples" post.


Rick Venable
computational chemist

Re: have trouble reading water molecules from pdb file
lqz #37262 01/07/19 07:45 PM
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rmv Offline
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In principle, you should be able to use the VMD generated PSF directly in CHARMM to read coordinates from a DCD file, avoiding the PDB import problem altogether.


Rick Venable
computational chemist

Re: have trouble reading water molecules from pdb file
lqz #37263 01/08/19 05:17 AM
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It seems the same problem as I have encountered.
please try: (you can get all the files from CHARMM-GUI)

! Read topology and parameter files
stream toppar.str

--------- in toppar.str ------------------------
* GENERATED BY CHARMM-GUI (http://www.charmm-gui.org) v2.0 on Dec, 31. 2018. JOBID=1546272907
* Stream file for topology and parameter reading
*

! protein topology and parameter
open read card unit 10 name toppar/top_all36_prot.rtf
read rtf card unit 10

open read card unit 20 name toppar/par_all36m_prot.prm
read para card unit 20 flex

! nucleic acids
open read card unit 10 name toppar/top_all36_na.rtf
read rtf card unit 10 append

open read card unit 20 name toppar/par_all36_na.prm
read para card unit 20 append flex

! carbohydrates
open read card unit 10 name toppar/top_all36_carb.rtf
read rtf card unit 10 append

open read card unit 20 name toppar/par_all36_carb.prm
read para card unit 20 append flex

...
...

! Additional topologies and parameters for water and ions
stream toppar/toppar_water_ions.str
stream toppar/toppar_dum_noble_gases.str

...
...
---------------------------


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