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#37533 - 06/24/19 11:31 AM phosphoserine parameter
nawel Offline
Forum Member

Registered: 05/14/19
Posts: 6
Dear charmm users, I have a ligand with a phosphoserine and a cap on N-ter.

I would like to create the psf file for my ligand but I encounter couple of errors:

Here is my input file:

* Create PSF
*

! Read RTF
open unit 1 card read name "/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/top_all27_prot_na.rtf"
read rtf card unit 1
close unit 1

! Read PARA
open unit 1 card read name "/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/par_all27_prot_na.prm"
read para card unit 1
close unit 1


! Read topology and parameter files for phosphoserine
open read card unit 10 name sep.rtf
read rtf card unit 10 append
close unit 10

open read card unit 10 name sep.prm
read para card unit 10 append
close unit 10


!stream /sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/stream/toppar_prot_na_all.str

!#### ligand ####
!####################

! Read PDB seq
open unit 1 card read name "lig_chimera.pdb"
read sequ pdb unit 1

generate ligand warn setup first ACE! Command to generate the psf


PATCH SP2 SER 4 SETUP WARN
AUTOGENERATE ANGLES DIHEDRALS


! Read PDB struct
rewind unit 1
read coor pdb unit 1
close unit 1


! Add missings atoms
ic fill
ic param
ic build
! Add hydrogens
hbuild sele hydro end


write psf card name ligand.psf
write coor card name ligand.cor
write coor pdb name ligand.pdb

! Write PSF
!OPEN UNIT 1 WRITe CARD NAME ligand.psf
!WRITe PSF CARD UNIT 1
!* PSF ligand HBR
!*

!OPEN UNIT 1 WRITe CARD NAME cor/ligand.pdb
!WRITe COOR PDB UNIT 1
!*PDB ligand_pdb ligand
!*

!OPEN UNIT 1 WRITe CARD NAME cor/ligand.cor
! WRITe COOR CARD UNIT 1
!*CRD ligand_crd ligand
! *


stop




but I get this output file:


1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 36b1 August 15, 2011
Git commit ID 093ce0e
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-573.18.1.el6.x86_64(x86_64)@pip
Created on 6/24/19 at 17:27:56 by user: mele

Maximum number of ATOMS: 360720, and RESidues: 120240
RDTITL> * CREATE PSF
RDTITL> *

CHARMM>

CHARMM> ! Read RTF
CHARMM> open unit 1 card read name "/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/top_all27_prot_na.rtf"
VOPEN> Attempting to open::/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/top_all27_prot_na.rtf::
OPNLGU> Unit 1 opened for READONLY access to /sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/top_all27_prot_na.rtf

CHARMM> read rtf card unit 1
MAINIO> Residue topology file being read from unit 1.
TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>> AND NUCLEIC ACIDS <<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> JULY, 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *

CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

CHARMM>

CHARMM> ! Read PARA
CHARMM> open unit 1 card read name "/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/par_all27_prot_na.prm"
VOPEN> Attempting to open::/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/par_all27_prot_na.prm::
OPNLGU> Unit 1 opened for READONLY access to /sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/par_all27_prot_na.prm

CHARMM> read para card unit 1

PARAMETER FILE BEING READ FROM UNIT 1
TITLE> *>>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>> AND NUCLEIC ACIDS <<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

CHARMM>

CHARMM>

CHARMM> ! Read topology and parameter files
CHARMM> open read card unit 10 name sep.rtf
VOPEN> Attempting to open::sep.rtf::
OPNLGU> Unit 10 opened for READONLY access to sep.rtf

CHARMM> read rtf card unit 10 append
MAINIO> Residue topology file being read from unit 10.
TITLE> * TOPOLOGY FOR PHOSPHORYLATED AMINO ACIDS
TITLE> *

CHARMM> close unit 10
VCLOSE: Closing unit 10 with status "KEEP"

CHARMM>

CHARMM> open read card unit 10 name sep.prm
VOPEN> Attempting to open::sep.prm::
OPNLGU> Unit 10 opened for READONLY access to sep.prm

CHARMM> read para card unit 10 append

PARAMETER FILE BEING READ FROM UNIT 10
TITLE> * ADDITIONAL PARAMETERS FOR PHOSPHORYLATED AMINO ACIDS
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM> close unit 10
VCLOSE: Closing unit 10 with status "KEEP"

CHARMM>

CHARMM>

CHARMM> !stream /sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/stream/toppar_prot_na_all.str
CHARMM>

CHARMM> !#### ligand ####
CHARMM> !####################
CHARMM>

CHARMM> ! Read PDB seq
CHARMM> open unit 1 card read name "ligand_N_c_TER_noh_chimera.pdb"
VOPEN> Attempting to open::ligand_N_c_TER_noh_chimera.pdb::
OPNLGU> Unit 1 opened for READONLY access to ligand_N_c_TER_noh_chimera.pdb

CHARMM> read sequ pdb unit 1
MAINIO> Sequence information being read from unit 1.
TITLE> *

RESIDUE SEQUENCE -- 3 RESIDUES
TRP PRO SER

CHARMM>

CHARMM> generate ligand warn setup first ACE! Command to generate the psf
THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE
THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP .
ATOMS "N " "-C " "CA " "HN " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER .
ATOMS "C " "+N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 SER .
ATOMS "O " "C " WERE REQUESTED.
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 SER .
ATOMS "C " "CA " "+N " "O " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 SER .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 SER .
ATOMS "O " "C " WERE REQUESTED.
GENPSF> Segment 1 has been generated. Its identifier is LIGAND.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 1 Number of residues = 3
Number of atoms = 56 Number of groups = 17
Number of bonds = 58 Number of angles = 103
Number of dihedrals = 154 Number of impropers = 7
Number of cross-terms = 2
Number of HB acceptors = 6 Number of HB donors = 4
Number of NB exclusions = 0 Total charge = -1.00000
QXFORM> Expanded format used.
More than 4 character SEGID used.

CHARMM> ! patch KCX HBR 73
CHARMM>

CHARMM> PATCH SP2 SER 4 SETUP WARN
** WARNING ** GETRSN could not find the SEGMENT SEG="SER " RES="4 "

***** LEVEL -3 WARNING FROM *****
***** Bad residue specified for patching
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5



/---------\
/ \
/ \
/ \
! XXXX XXXX !
! XXXX XXXX !
! XXX XXX !
! X !
--\ XXX /--
! ! XXX ! !
! ! ! !
! I I I I I !
! I I I I !
\ /
-- --
\---/
XXX XXX
XXXX XXXX
XXXXX XXXXX
XXX XXX
XXX XXX
XXXXX
XXX XXX
XXX XXX
XXX XXX
XXXXX XXXXX
XXXX XXXX
XXX XXX


Execution terminated due to the detection of a fatal error.

ABNORMAL TERMINATION
MOST SEVERE WARNING WAS AT LEVEL -3

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 0.83 SECONDS
CPU TIME: 0.76 SECONDS


Can anyone help me with the correct procedure to follow?

Many thanks,

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#37534 - 06/24/19 01:36 PM Re: phosphoserine parameter [Re: nawel]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4727
Loc: ~ 59N, 15E
Use the most recent version of CHARMM, it is free to download. C36 is very, very old.

Use the CHARMM 36 force field.
In this FF the phosphoserine patch is found in:
toppar/stream/prot/toppar_all36_prot_na_combined.str
Use
read rtf/para/coor/psf card name <filename>
instead of the super-obsolete, and error prone, series of commands: open, read, close

The patch command needs one (or more) SEGID and RESID to identify the residue that should be pathced; you have specified a residue name and number. The error message is quite clear.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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