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Hi rmv, i have gone through your script could not understand below part read univ * modified pdb * pdb segid 22 1 ires 23 4 w 61 6 end Also i am having problem with my water box which i created using charmm-GUI. dims 30*30*30. The problem is i am getting two segid in the box and am not able to create psf for the pdb. this is the small part of my water box ATOM 1591 OH2 TIP3 541 6.691 5.318 1.346 1.00 0.00 WZ1
ATOM 1592 H1 TIP3 541 6.325 4.552 1.788 1.00 0.00 WZ1
ATOM 1593 H2 TIP3 541 7.604 5.347 1.632 1.00 0.00 WZ1
ATOM 1594 OH2 TIP3 542 8.664 4.668 2.881 1.00 0.00 WZ1
ATOM 1595 H1 TIP3 542 9.563 4.394 2.697 1.00 0.00 WZ1
ATOM 1596 H2 TIP3 542 8.277 3.926 3.346 1.00 0.00 WZ1
ATOM 1597 OH2 TIP3 1 -3.044 -4.896 10.643 1.00 0.00 WZ2
ATOM 1598 H1 TIP3 1 -2.955 -3.952 10.510 1.00 0.00 WZ2
ATOM 1599 H2 TIP3 1 -3.683 -5.171 9.985 1.00 0.00 WZ2
ATOM 1600 OH2 TIP3 2 -4.111 -5.641 14.062 1.00 0.00 WZ2
ATOM 1601 H1 TIP3 2 -4.150 -6.287 14.767 1.00 0.00 WZ2
ATOM 1602 H2 TIP3 2 -4.434 -6.107 13.290 1.00 0.00 WZ2
ATOM 1603 OH2 TIP3 4 -0.405 -2.702 12.363 1.00 0.00 WZ2
ATOM 1604 H1 TIP3 4 -0.846 -3.422 12.814 1.00 0.00 WZ2
ATOM 1605 H2 TIP3 4 -0.418 -1.981 12.993 1.00 0.00 WZ2 i would like to have only 1 segid in my pdb as well as psf. ! Read sequence from pdb file, generate segment, and read coordinates. open read card name "waterbox.pdb" unit 12 read segid WZ1 PDB unit 12 but it reads all 855 residues instead of only reading segment WZ1 which has 542 water molecules. How can i create pdb as well as psf from above pdb in charmm to get single segid for whole water box. Thank-you, Regards, Rohit
Last edited by Rohit; 11/23/17 05:57 AM.
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Please note that as indicated in the READ BEFORE POSTING topic, duplicate posts are not permitted, so the other one was removed. The description at the beginning of the complex PDB input examples post is fairly clear about the need to put separate segments in separate files to use those examples as a template for your own work. See io.doc for a more complete description of the READ UNIV facility. It can be used to read a multiple segment PDB, as outlined in the second example of the UNIVersal coord reader examples post.
Rick Venable
computational chemist
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Thank-you, it increased my understanding a bit, still i need to change the single pdb to 2 pdbs which i wanted to avoid. I still dont understand why charmm-gui would create 2 segments in water box. what purpose does it serve ?
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Note that the READ SEQUence PDB command has several options that allow you to fine tune what is to be read from the file. Excerpt from io.doc:
The SEGI <segid> option allows the sequence to be read only for the residues
belonging to the corresponding segid in the coordinate file.
For the PDB option resids are always read from the resSeq (resid) field.
This is useful when one wants to specify residue names (rather than use
the number representation). No other information is read from the coordinate
file during this process. To read the sequence for a specific chain in a PDB
file the CHAIn <char> option can be used; <char> is the one letter PDB chain
id in position 22 of ATOM/HETATM records. If the SEGI <segid> option is used
the sequence is read for the atoms that have the corresponding segid in
columns 73-76 of the PDB file. NCHAin <int> starts reading from chain number
<int> as defined by TER separator records. Variables SQNRES and SQRESID are
set to the number of residues read and the SEGId used.
There are simple examples in the Script Archive forum of how to set up a waterbox.
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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even if i write
read sequence segi WZ1 unit 12
it gives error because i am not specifying number of residues to be read.
I tried
read sequence TIPS segi WZ1 unit 12
this is also not working.
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How about
READ SEQU PDB SEGI WZ1 NAME waterbox.pdb
GENE WZ1 NOANGLE NODIHE
READ SEQU PDB SEGI WZ2 NAME WATERBOX.PDB
GENE WZ2 NOANGLE NODIHE
See also the testcase ~charmm/test/c39test/readpdb.inp
If all you have is water this should also work:
read sequ tip3 542
GENE WZ1 NOANGLE NODIHE
read sequ tip3 313
GENE WZ2 NOANGLE NODIHE
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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The first one is not working 2nd option works. below is the inp i used open read card name "waterbox.pdb" unit 12
read sequ tip3 532
GENE BOX NOANGLE NODIHE
read sequ tip3 323
GENE BOX1 NOANGLE NODIHE
!generate box setup first none last none noangle nodihedrals
!rewind unit 12
read coor pdb unit 12
!open read card name "waterbox_watb.pdb" unit 13
!read sequence PDB unit 13
!generate box1 setup first none last none noangle nodihedrals
!rewind unit 13
!read coor pdb offs 532 unit 13
join box box1 renum
open unit 25 card write name "waterbox.psf"
write psf card xplor unit 25
* PSF
* error message while reading coordinates. CHARMM> !generate box setup first none last none noangle nodihedrals
CHARMM> !rewind unit 12
CHARMM> read coor pdb unit 12
read CHARMM-pdb format
SPATIAL COORDINATES BEING READ FROM UNIT 12
TITLE> EQUILIBRATED WATER
TITLE> DATE: 11/20/17 4:21:35 CREATED BY USER: APACHE
TITLE> *
** WARNING ** After reading, there are no coordinates for selected atom: 457 153 TIP3 OH2
** WARNING ** After reading, there are no coordinates for selected atom: 458 153 TIP3 H1
** WARNING ** After reading, there are no coordinates for selected atom: 459 153 TIP3 H2
** WARNING ** After reading, there are no coordinates for selected atom: 469 157 TIP3 OH2
** WARNING ** After reading, there are no coordinates for selected atom: 470 157 TIP3 H1
** WARNING ** After reading, there are no coordinates for selected atom: 471 157 TIP3 H2
** WARNING ** After reading, there are no coordinates for selected atom: 643 215 TIP3 OH2
** WARNING ** After reading, there are no coordinates for selected atom: 644 215 TIP3 H1
** WARNING ** After reading, there are no coordinates for selected atom: 645 215 TIP3 H2
** WARNING ** After reading, there are no coordinates for selected atom: 928 310 TIP3 OH2
** A total of 963 selected atoms have no coordinates
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No need for all those error-prone OPEN statements, you can simply use the form READ ... NAME WATERBOX.PDB
Are there coordinates for those water molecules in your PDB-file?
Which CHARMM version are you using?
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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the coordinates are there, i dont know why it gives error so i tried reading crd file now it is working fine.
I am using c37a2 charmm
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You are using a very old, developmental version. Upgrade! The most recent version is available for download (for free) here: http://charmm.chemistry.harvard.edu/charmm_lite.php
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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