Generating pdb, crd and psf for a peptide sequence
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Top level: CHARMM
Below script does for CHARMM what Leap does for AMBER (see Setting_up) -- generates input files given a peptide sequence. Here, it generates structure (pdb and crd) and topology (psf) files for Alanine Dipeptide. Search for TOSET for instructions to customize for your sequence.
! Warning level, -5 = very lax BOMLev -5 ! Verbosity level, 0 = small ! PRNLEV 0 ! set molname <TOSET:prefix for file names> set molname aladipeptide ! SET PATH to topology and parameter files ! quotes MUST if path has both upper and lower case letters ! set pardir <TOSET> set pardir "/home/ss2029/svn/CHARMM31/toppar" ! READ TOPOLOGY open unit 1 read formatted name @pardir/"top_all22_prot.inp" read rtf card unit 1 close unit 1 ! READ PARAMS open unit 2 read formatted name @pardir/"par_all22_prot.inp" read para card unit 2 close unit 2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! CONSTRUCT STRUCTURE FROM SEQUENCE ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! TOSET: number of residues in third line and sequence in 3-letter code in fourth ! last line of this block adds on the terminal groups - first like for ACE and CT3; second for NTER and CTER READ SEQUence CARD * 1 ALA GENErate alad FIRSt ACE LAST CT3 WARN SETUp !GENErate alad FIRS NTER LAST CTER SETUp !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! TWEAK INTERNAL COORDINATE ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! this is alanine dipeptide specific - check for your system IC PARAMETERS IC PURGE IC EDIT DIHE 1 CY 1 N 1 CA 1 C -82.7 DIHE 1 N 1 CA 1 C 1 NT 73.5 END PRINT IC IC SEED 1 N 1 CA 1 C IC BUILD !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! WRITE CRD PDB AND PSF ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! write crd open UNIT 20 NAME @molname.crd WRITE CARD WRITE COOR UNIT 20 CARD CLOSE UNIT 20 ! write pdb open UNIT 20 NAME @molname.pdb WRITE CARD WRITE COOR UNIT 20 PDB CLOSE UNIT 20 ! write psf open UNIT 20 NAME @molname.psf WRITE CARD WRITE PSF CARD UNIT 20 CLOSE UNIT 20
Execute on the command line as
$ ~/svn/CHARMM31/exec/gnu/charmm < createPdbPdf.inp
If all goes well, the stdout will be
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 31a2 February 15, 2004
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.11.4-21.17-smp(x86_64)@clust.ch.ca
Created on 6/22/11 at 17: 1:15 by user: ss2029
Maximum number of ATOMS: 25140, and RESidues: 14000
Current HEAP size: 2048000, and STACK size: 500000
RDTITL> BOMLEV -5
RDTITL> No title read.
***** LEVEL 1 WARNING FROM <RDTITL> *****
***** Title expected.
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5
CHARMM> BOMLev -5
CHARMM>
CHARMM> ! Verbosity level, 0 = small
CHARMM> ! PRNLEV 0
CHARMM>
CHARMM> ! set molname <TOSET:prefix for file names>
CHARMM> set molname aladipeptide
Parameter: MOLNAME <- "ALADIPEPTIDE"
CHARMM>
CHARMM> ! SET PATH to topology and parameter files
CHARMM> ! quotes MUST if path has both upper and lower case letters
CHARMM> ! set pardir <TOSET>
CHARMM> set pardir "/home/ss2029/svn/CHARMM31/toppar"
Parameter: PARDIR <- ""/home/ss2029/svn/CHARMM31/toppar""
:
:
:
CHARMM> ! write psf
CHARMM> open UNIT 20 NAME @molname.psf WRITE CARD
Parameter: MOLNAME -> "ALADIPEPTIDE"
VOPEN> Attempting to open::aladipeptide.psf::
OPNLGU> Unit 20 opened for WRITE access to aladipeptide.psf
CHARMM> WRITE PSF CARD UNIT 20
RDTITL> CLOSE UNIT 20
RDTITL> No title read.
CHARMM> CLOSE UNIT 20
VCLOSE: Closing unit 20 with status "KEEP"
$$$$$$ New timer profile $$$$$
Total time 0.34631 Other: 0.00000
NORMAL TERMINATION BY END OF FILE
MAXIMUM STACK SPACE USED IS 47526
STACK CURRENTLY IN USE IS 0
MOST SEVERE WARNING WAS AT LEVEL 1
HEAP PRINTOUT- HEAP SIZE 2048000
SPACE CURRENTLY IN USE IS 0
MAXIMUM SPACE USED IS 3772
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 2048000 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 0.35 SECONDS
CPU TIME: 0.00 SECONDS
and following three files will be generated
1. aladipeptide.crd
* NONE *
* DATE: 6/22/11 17: 1:15 CREATED BY USER: ss2029
*
22
1 1 ALA CAY -2.15972 0.13645 1.06514 ALAD 1 0.00000
2 1 ALA HY1 -2.46595 0.00075 0.00583 ALAD 1 0.00000
3 1 ALA HY2 -2.56186 1.09960 1.44586 ALAD 1 0.00000
4 1 ALA HY3 -2.56186 -0.69963 1.67635 ALAD 1 0.00000
5 1 ALA CY -0.67250 0.14801 1.15536 ALAD 1 0.00000
6 1 ALA OY -0.10455 0.28664 2.23754 ALAD 1 0.00000
7 1 ALA N 0.00000 0.00000 0.00000 ALAD 1 0.00000
8 1 ALA HN -0.45263 -0.11288 -0.88113 ALAD 1 0.00000
9 1 ALA CA 1.43000 0.00000 0.00000 ALAD 1 0.00000
10 1 ALA HA 1.78325 -0.49652 0.89651 ALAD 1 0.00000
11 1 ALA CB 1.91950 -0.83356 -1.20665 ALAD 1 0.00000
12 1 ALA HB1 1.48454 -1.85447 -1.15533 ALAD 1 0.00000
13 1 ALA HB2 1.59875 -0.37311 -2.16656 ALAD 1 0.00000
14 1 ALA HB3 3.02650 -0.93210 -1.21396 ALAD 1 0.00000
15 1 ALA C 2.04647 1.35649 0.00000 ALAD 1 0.00000
16 1 ALA O 3.26842 1.49701 0.00000 ALAD 1 0.00000
17 1 ALA NT 1.98354 2.04429 1.15412 ALAD 1 0.00000
18 1 ALA HNT 1.55206 1.68456 1.97779 ALAD 1 0.00000
19 1 ALA CAT 2.55151 3.35399 1.23782 ALAD 1 0.00000
20 1 ALA HT1 2.05548 4.02113 0.50080 ALAD 1 0.00000
21 1 ALA HT2 2.40207 3.75828 2.26181 ALAD 1 0.00000
22 1 ALA HT3 3.63888 3.30154 1.01599 ALAD 1 0.00000
2. aladipeptide.pdb
REMARK NONE * REMARK DATE: 6/22/11 17: 1:15 CREATED BY USER: ss2029 ATOM 1 CAY ALA 1 -2.160 0.136 1.065 1.00 0.00 ALAD ATOM 2 HY1 ALA 1 -2.466 0.001 0.006 1.00 0.00 ALAD ATOM 3 HY2 ALA 1 -2.562 1.100 1.446 1.00 0.00 ALAD ATOM 4 HY3 ALA 1 -2.562 -0.700 1.676 1.00 0.00 ALAD ATOM 5 CY ALA 1 -0.672 0.148 1.155 1.00 0.00 ALAD ATOM 6 OY ALA 1 -0.105 0.287 2.238 1.00 0.00 ALAD ATOM 7 N ALA 1 0.000 0.000 0.000 1.00 0.00 ALAD ATOM 8 HN ALA 1 -0.453 -0.113 -0.881 1.00 0.00 ALAD ATOM 9 CA ALA 1 1.430 0.000 0.000 1.00 0.00 ALAD ATOM 10 HA ALA 1 1.783 -0.497 0.897 1.00 0.00 ALAD ATOM 11 CB ALA 1 1.919 -0.834 -1.207 1.00 0.00 ALAD ATOM 12 HB1 ALA 1 1.485 -1.854 -1.155 1.00 0.00 ALAD ATOM 13 HB2 ALA 1 1.599 -0.373 -2.167 1.00 0.00 ALAD ATOM 14 HB3 ALA 1 3.026 -0.932 -1.214 1.00 0.00 ALAD ATOM 15 C ALA 1 2.046 1.356 0.000 1.00 0.00 ALAD ATOM 16 O ALA 1 3.268 1.497 0.000 1.00 0.00 ALAD ATOM 17 NT ALA 1 1.984 2.044 1.154 1.00 0.00 ALAD ATOM 18 HNT ALA 1 1.552 1.685 1.978 1.00 0.00 ALAD ATOM 19 CAT ALA 1 2.552 3.354 1.238 1.00 0.00 ALAD ATOM 20 HT1 ALA 1 2.055 4.021 0.501 1.00 0.00 ALAD ATOM 21 HT2 ALA 1 2.402 3.758 2.262 1.00 0.00 ALAD ATOM 22 HT3 ALA 1 3.639 3.302 1.016 1.00 0.00 ALAD TER 23 ALA 1 END
and
3. aladipeptide.psf
PSF CMAP CHEQ
2 !NTITLE
* NONE *
* DATE: 6/22/11 17: 1:15 CREATED BY USER: ss2029
22 !NATOM
1 ALAD 1 ALA CAY 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
2 ALAD 1 ALA HY1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
3 ALAD 1 ALA HY2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
4 ALAD 1 ALA HY3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
5 ALAD 1 ALA CY 20 0.510000 12.0110 0 0.00000 -0.301140E-02
6 ALAD 1 ALA OY 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
7 ALAD 1 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
8 ALAD 1 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
9 ALAD 1 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
10 ALAD 1 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
11 ALAD 1 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
12 ALAD 1 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
13 ALAD 1 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
14 ALAD 1 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
15 ALAD 1 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
16 ALAD 1 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
17 ALAD 1 ALA NT 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
18 ALAD 1 ALA HNT 1 0.310000 1.00800 0 0.00000 -0.301140E-02
19 ALAD 1 ALA CAT 24 -0.110000 12.0110 0 0.00000 -0.301140E-02
20 ALAD 1 ALA HT1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
21 ALAD 1 ALA HT2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
22 ALAD 1 ALA HT3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
21 !NBOND: bonds
5 1 5 7 1 2 1 3
1 4 6 5 11 9 7 8
7 9 15 9 9 10 11 12
11 13 11 14 16 15 15 17
17 18 17 19 19 20 19 21
19 22
36 !NTHETA: angles
2 1 3 2 1 4 2 1 5
3 1 4 3 1 5 4 1 5
1 5 6 1 5 7 6 5 7
5 7 8 5 7 9 8 7 9
7 9 10 7 9 11 7 9 15
10 9 11 10 9 15 11 9 15
9 11 12 9 11 13 9 11 14
12 11 13 12 11 14 13 11 14
9 15 16 9 15 17 16 15 17
15 17 18 15 17 19 18 17 19
17 19 20 17 19 21 17 19 22
20 19 21 20 19 22 21 19 22
42 !NPHI: dihedrals
1 5 7 8 1 5 7 9
2 1 5 6 2 1 5 7
3 1 5 6 3 1 5 7
4 1 5 6 4 1 5 7
5 7 9 10 5 7 9 11
5 7 9 15 6 5 7 8
6 5 7 9 7 9 11 12
7 9 11 13 7 9 11 14
7 9 15 16 7 9 15 17
8 7 9 10 8 7 9 11
8 7 9 15 9 15 17 18
9 15 17 19 10 9 11 12
10 9 11 13 10 9 11 14
10 9 15 16 10 9 15 17
11 9 15 16 11 9 15 17
12 11 9 15 13 11 9 15
14 11 9 15 15 17 19 20
15 17 19 21 15 17 19 22
16 15 17 18 16 15 17 19
18 17 19 20 18 17 19 21
18 17 19 22 19 17 15 9
4 !NIMPHI: impropers
5 1 7 6 7 5 9 8
17 15 19 18 15 9 17 16
2 !NDON: donors
7 8 17 18
2 !NACC: acceptors
6 5 16 15
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0
6 0 !NGRP NST2
0 1 0 4 1 0 6 1 0
10 1 0 14 1 0 16 1 0
1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1
0 0 !NUMLP NUMLPH
0 !NCRTERM: cross-terms
See clust:/home/ss2029/WORK/DEMOS/CHARMMSCRIPTS for more sample CHARMM input files.
Top level: CHARMM
--Ss2029 15:29, 22 June 2011 (UTC)