From: Ian Bongalonta (ianbongalonta_at_gmail.com)
Date: Wed Sep 07 2022 - 20:29:39 CDT
Hi everyone,
I am relatively new to NAMD and am attempting to use psfgen read in the
topology of CHARMM36 files in order to patch tyrosine to deprotonate it.
I've downloaded the files top_all36_prot.rtf and
protpatch_protein_toppar36.str from the official CHARMM website, but they
seem to be formatted differently.
A patch from top_all36_prot.rtf looks like:
PRES NTER 1.00 ! standard N-terminus
GROUP ! use in generate statement
ATOM N NH3 -0.30 !
ATOM HT1 HC 0.33 ! HT1
ATOM HT2 HC 0.33 ! (+)/
ATOM HT3 HC 0.33 ! --CA--N--HT2
ATOM CA CT1 0.21 ! | \
ATOM HA HB1 0.10 ! HA HT3
DELETE ATOM HN
BOND HT1 N HT2 N HT3 N
DONOR HT1 N
DONOR HT2 N
DONOR HT3 N
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
While a patch from protpatch_protein_toppar36.str looks like:
! Deprotonated tyrosine (TYR)
! This is the patch for deprotonated tyrosine. The HH atom was deleted
pres tyru -1
! | HD1 HE1M
! HN-N | |
! | HB1 CD1--CE1M
! | | // \\
! HA-CA--CB--CG CZM--OHM
! | | \ __ /
! | HB2 CD2--CE2M
! O=C | |
! | HD2 HE2M
group
atom ce1m ca -0.60 ce1 he1 ce2 he2 cz oh hh
atom he1m hp 0.28 ce1 he1 ce2 he2 cz oh hh
group
atom ce2m ca -0.60 ce1 he1 ce2 he2 cz oh hh
atom he2m hp 0.28 ce1 he1 ce2 he2 cz oh hh
group
atom czm ca 0.40 ce1 he1 ce2 he2 cz oh hh
atom ohm oh1 -0.76 ce1 he1 ce2 he2 cz oh hh
bond cd1 ce1m
bond ce1m he1m
bond ce1m czm
bond czm ohm
bond czm ce2m
bond cd2 ce2m
bond ce2m he2m
While the program seems to be able to handle top_all36_prot.rtf just fine
(and I've used it several times before), when I read in the topology for
protpatch_protein_toppar36.str:
package require psfgen
topology protpatch_protein_toppar36.str
it gives me the following error:
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 56 CPUs detected.
Info) Free system memory: 124423MB (48%)
Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Info) Dynamically loaded 2 plugins in directory:
Info) /software/vmd-1.9.2-x86_64/lib/plugins/LINUXAMD64/molfile
1.6.2
psfgen) reading topology file protpatch_protein_toppar36.str
psfgen) Patches to acheive charged and uncharged amino acids D, E, H and K
psfgen) Contact C.L. Brooks III for additional information
psfgen)
psfgen) reading topology from stream file
psfgen) title
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) ERROR! Explicit exclusions or fluctuating charges not supported,
atom ignored.
psfgen) skipping parameters in stream file
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
psfgen) ERROR! FAILED TO RECOGNIZE ECHO
I understand that the error is likely due to the change in format (forgive
me, as I'm pretty new), and I could attempt to copy the format of the
patch, but is there a way to do this automatically and more easily?
Thank you!
Ian Bongalonta
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