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ERROR in RTFRD when reading top_all36_prot.rtf
#37926 06/12/20 08:55 AM
Joined: Jun 2020
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cm14sjm Offline OP
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Hi

I'm new to CHARMM and am having some problems getting a minimisation script to run.

I downloaded a pod file from the PBD then used the CHARMM GUI solution builder to get the minimisation in explicit solvent and production inputs. But, when I try run the minimisation script I get lots of RTFRDR about errors when trying to read the topology files. I have had a look on some other threads regarding similar errors, but am still struggling to fix the problem

I used the CHARMM36m forcefield options and I have c37a1dev version of CHARMM.


Below is the input script and output errors:


DIMENS CHSIZE 4200000 MAXRES 3000000

! Read topology and parameter files
stream toppar.str

! Read PSF and Coordinates
open read unit 10 card name ../step3_pbcsetup.psf
read psf unit 10 card
open read unit 10 card name ../step3_pbcsetup.crd
read coor unit 10 card
!
! Setup PBC (Periodic Boundary Condition)
!

stream ../step3_pbcsetup.str

open read unit 10 card name ../crystal_image.str
CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma
CRYSTAL READ UNIT 10 CARD

!Image centering by residue
calc xcen = @A / 2
calc ycen = @B / 2
calc zcen = @C / 2
coor translate xdir @xcen ydir @ycen zdir @zcen
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname TIP3 end
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele ( segid @posid .or. segid @negid ) end

!
! Nonbonded Options
!

omm on

nbonds atom vatom vfswitch bycb -
ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 -
inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6
energy

!
!use positional restraints for equilibration
![you can change the force constant and run longer equilibration (at least 100-200 ps)]
!

define PROT sele ( segid PROA ) end
define CARB sele none end
define HETE sele none end

define BB sele ( ( type C .or. type O .or. type N .or. type CA .or. -
type P .or. type O1P .or. type O2P .or. type O5' .or. -
type C5' .or. type C4' .or. type C3' .or. type O3' ) .and. PROT ) .or. -
( ( type C+ .or. ( type O5 .and. .bonded. type C1 ) .or. ( type O6 .and. .bonded. type C2 ) ) .and. CARB ) .or. -
( .not. hydrogen .and. HETE ) end
define SC sele .not. BB .and. .not. hydrogen .and. ( PROT .or. CARB ) end

cons harm force 1.0 sele BB end
cons harm force 0.1 sele SC end

mini SD nstep 50 nprint 5
mini ABNR nstep 50 nprint 5

!
! NVT dynamics,
! you can change
! nstep : number of MD steps
! nprint : print-out frequency
! NOTE:
! The integration time step (timestep) is set to 1 fs only for equilibration
! to avoid any unstable dynamics and thus abnormal termination.
! However, it might be possible to increase it to 2 fs in most applications.
!

set nstep = 125000

set temp = 303.15
shake bonh param fast

open write unit 12 card name step4_equilibration.rst

DYNA leap start timestep 0.001 nstep @nstep -
nprint 1000 iprfrq 1000 ntrfrq 1000 -
iunread -1 iunwri 12 iuncrd -1 iunvel -1 kunit -1 -
nsavc 0 nsavv 0 -
omm langevin gamma 10 firstt @temp finalt @temp

open write unit 10 card name step4_equilibration.pdb
write coor unit 10 pdb

open write unit 10 card name step4_equilibration.crd
write coor unit 10 card
close unit 10

stop




Output errors:



CHARMM> ! Read topology and parameter files
CHARMM> stream toppar.str
VOPEN> Attempting to open::toppar.str::
OPNLGU> Unit 99 opened for READONLY access to toppar.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON JUN, 10. 2020. JOBID=9179077883
RDTITL> * STREAM FILE FOR TOPOLOGY AND PARAMETER READING
RDTITL> *
Parameter: IN1 <- ""

CHARMM>

CHARMM> ! protein topology and parameter
CHARMM> open read card unit 10 name ../toppar/top_all36_prot.rtf
VOPEN> Attempting to open::../toppar/top_all36_prot.rtf::
OPNLGU> Unit 10 opened for READONLY access to ../toppar/top_all36_prot.rtf

CHARMM> read rtf card unit 10
MAINIO> Residue topology file being read from unit 10.
TITLE> *>>>>>>>>CHARMM36 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<

**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
MASS -1 H 1.00800
**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
MASS -1 HC 1.00800


....


**** ERROR in RTFRDR **** The atom type code, NH1 is unknown. The atom will be ignored.
ATOM N NH1 -0.47
**** ERROR in RTFRDR **** The atom type code, H is unknown. The atom will be ignored.
ATOM HN H 0.31


I get these errors for what looks like every atom I have in my protein.

There were 13 warning(s) from RTFRDR.
There were 578 error(s) from RTFRDR.
Execution will be terminated.


Thank you in advance or any help

Re: ERROR in RTFRD when reading top_all36_prot.rtf
cm14sjm #37927 06/12/20 03:09 PM
Joined: Sep 2003
Posts: 8,470
rmv Online Content
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Online Content
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Joined: Sep 2003
Posts: 8,470
You need a newer CHARMM version, one that supports the generic -1 as the atom type code.


Rick Venable
computational chemist


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