From: Zhilei Chen (zchen4_at_students.uiuc.edu)
Date: Tue Nov 04 2003 - 09:48:01 CST
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
>>
>>
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