From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Sep 08 2022 - 11:04:17 CDT
Hi Ian,
I believe your actual problem is that .str files can contain Charmm and
shell commands which cannot be parsed by psfgen. You would need to comment
out the non RES and PRES entries for proper function.
HTH,
Brian
On Wed, Sep 7, 2022, 9:36 PM Ian Bongalonta <ianbongalonta_at_gmail.com> wrote:
> 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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