RE: Question about AUTOGENERATE

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Nov 04 2003 - 10:24:58 CST

Hello,

Do you have a mass entry for the N2 nitrogen in the topology file
corresponding to the one listed in your pdb file?
The structure of the topology file you listed below is not standard and
may be another source of your troubles. The residue keyword should be
directly before the group keyword, at least that is how it is found
throughout all the topology files that I have seen, but my experience is
limited.
Futhermore, it is helpful (if not required) to have the residue definition
in the topology file follow the same order as the the atoms in the pdb
file you are reading from.

Just my .02
Brian

 On Tue, 4 Nov 2003, Zhilei Chen wrote:

> Hi,
>
> I am using CHARMM 22 force field. I fixed the autogenerate command as
> recommend, but I am still having problem to generate the pdb and psf file.
>
> I generate the pdb file through MOE and I manually changed the atom name to
> match the topology file. (the pdb file generated by moe use the atom type as
> the atom name)
> Here I copied a few lines from my pdb file:
>
> -------------------------------
> ATOM 1 C5 BTN 1 0.163 -0.562 -0.563 0.00 C
>
> ATOM 2 H14 BTN 1 0.803 -1.338 -0.892 0.00 H
>
> ATOM 3 C4 BTN 1 0.361 0.680 -1.453 0.00 C
>
> ATOM 4 H13 BTN 1 0.794 0.388 -2.374 0.00 H
>
> ATOM 5 N2 BTN 1 -1.000 1.131 -1.677 0.00 N
>
> ATOM 6 H20 BTN 1 -1.172 2.059 -2.032 0.00 H
>
> ATOM 7 C3 BTN 1 -1.906 0.168 -1.351 0.00 C
>
> ATOM 8 O3 BTN 1 -3.104 0.216 -1.565 0.00 O
>
> ATOM 9 C2 BTN 1 1.286 1.670 -0.742 0.00 C
>
> ATOM 10 H10 BTN 1 2.261 1.264 -0.826 0.00 H
>
> ATOM 11 C6 BTN 1 0.491 -0.224 0.900 0.00 C
>
> ATOM 12 H11 BTN 1 -0.318 -0.513 1.519 0.00 H
>
> ATOM 13 H12 BTN 1 1.364 -0.746 1.194 0.00 H
>
> ATOM 14 S1 BTN 1 0.757 1.565 0.989 0.00 S
>
> -----------------------------------
> And here are some of the topology file I used
>
> ---------------------------------------
> AUTOGENERATE ANGLES DIHEDRALS
>
> RESIDUE BTN
>
> MASS 500 HN2 1.00800 H !
> MASS 501 NN2U 14.00700 N !
> MASS 502 ON1 15.99900 O !
> MASS 503 CN1 12.01100 C !
> GROUP
> ATOM C1 CD 0.754623
> ATOM C10 CT2 -0.379505
> ATOM C9 CT2 -0.338964
> ATOM C8 CT2 -0.308377
> ATOM C7 CT2 -0.296230
> ATOM C2 CP1 -0.350298
> ATOM C6 CP3 -0.468720
> ATOM C4 CP1 0.008080
> ATOM C5 CP1 0.043754
> ATOM C3 CN1 0.986269
> ATOM O1 OH1 -0.701422
> ATOM O2 OB -0.578268
> ATOM O3 ON1 -0.648188
> ATOM N1 NN2U -0.691553
> ATOM N2 NN2U -0.742907
>
> ......
> BOND C1 O1 ! 1.322486 CD OB
> BOND C1 O2 ! 1.219022 CD OH1
> BOND O1 H17 ! 1.499863 OH1 H
> BOND C1 C10 ! 1.531036 CD CT2
> BOND C10 H2 ! 1.099801 CT2 HA
> BOND C10 H3 ! 1.090048
> BOND C9 C10 ! 1.568060 CT2 CT2
> BOND C9 H4 ! 1.089189
> BOND C9 H5 ! 1.090360
> BOND C8 C9 ! 1.528866 CT2 CT2
> BOND C8 H6 ! 1.089215
> BOND C8 H7 ! 1.090249
> BOND C7 C8 ! 1.557578 CT2 CT2
>
> -----------------------------------
> I made sure all the atoms exist in the pdb file have their definition in the
> topology file. But when I try to generate the topology file, it can extracted
> the residue from the pdb file, but then....
>
> ---------------------------------------
> Info: generating structure...
> no atom C in residue BTN:1 of segment BIOT
> Warning: add conformation failed in patch NTER
> Info: segment complete.
> reading coordinates from pdb file ../biotin2.pdb for segment biot
> Warning: failed to set coordinate for atom 5 BTN:1 BIOT
> ...............
>
> ----------------------------
> I don't know what is the problem and I would really appreciate somebody can
> help me out.
>
> zhilei
>
>
> ====================================================
>
>
>
>
>
> >===== Original Message From Jim Phillips <jim_at_ks.uiuc.edu> =====
> >Hi,
> >
> >Psfgen is a black box implementation of a CHARMM topology file parser, and
> >it was based on the standard CHARMM 22/27 force field files. Therefore
> >it's not going to get some uncommon features or syntax right.
> >
> >You can fix the autogenerate command by changing it to this:
> >
> >AUTOGENERATE ANGLES DIHEDRALS
> >
> >The CHARMM 19 force field used explicit exclusions for some residues,
> >indicated by extra atom names on the ATOM line, such as (in TRP):
> >
> >ATOM CG C -0.03 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2
> >ATOM CD2 C 0.10 NE1 CE2 CE3 CZ2 CZ3 CH2
> >ATOM CE2 C -0.04 CE3 CZ2 CZ3 CH2
> >ATOM CE3 CR1E -0.03 CZ2 CZ3 CH2
> >
> >This is no longer the case with CHARMM 22/27, and therefore psfgen does
> >not implement explicit exclusions. It does (as of NAMD 2.5) notice that
> >these exclusions are present and ignores those atoms, which should
> >generate a fatal error if you try to use that residue.
> >
> >If you need CHARMM 19 or some other topology with explicit exclusions, you
> >can still use CHARMM (the program) to build psf and pdb files, and NAMD
> >should handle the explicit exclusions correctly. If being able to do
> >explicit exclusions in psfgen is critical for your resesarch, let your
> >voices be heard and I'll look into it.
> >
> >-Jim
> >
> >
> >On Mon, 3 Nov 2003, Zhilei Chen wrote:
> >
> >> Hi,
> >>
> >> I am a beginner of namd.
> >>
> >> I used the topology file from a previous paper as a exercise. It contains a
> >> command line
> >>
> >> AUTOGENERATE ANGLES=TRUE DIHEDRALS=TRUE END
> >>
> >> I am not sure what it does, but when I use psfgen, it keeps popping up
> >>
> >> ERROR! Failed to parse autogenerate statement.
> >> ERROR! Explicit exclustions not supported, atom ignored.
> >> ERROR! Explicit exclustions not supported, atom ignored.
> >> ................
> >>
> >> Can anyone help me?
> >> I am stuck:(
> >>
> >> zhilei
> >>
> >>
>
>

-- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **
*****************************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:17:53 CST