CHARMM Development Project
Posted By: Tarsis Patch for N-sultated Glucosamine - part 2 - 08/21/13 03:53 PM
Hi all,

After setting up the patch for adding the sulfamate to the N- glucosamine, I got the folloing error:

CHARMM> patch nhshb S 2 setup
ATOM S AGLCNA 2 S ADDED.
ATOM S AGLCNA 2 O2 ADDED.
ATOM S AGLCNA 2 O7 ADDED.
ATOM S AGLCNA 2 O8 ADDED.

Message from MAPIC: Atom numbers are changed.
*** LEVEL -3 WARNING *** BOMLEV IS -3
BOMLEV HAS BEEN SATISFIED.supposedly TERMINATING.

I cannot explain which atom numbers changed and why. The patch supposedly adds SO3 to the AGLCNA already deacetylated by another patch.

Thank in advance

Tarsis

Attached File
patch.tar.gz  (784 downloads)
Attached File
nhshb.out.txt  (813 downloads)
Attached File
NHSSHB.txt  (859 downloads)
Posted By: Kenno Re: Patch for N-sultated Glucosamine - part 2 - 08/21/13 05:11 PM
WRNLEV 1 BOMLEV -3 = . Sorry, you're on your own. Please review the READ THIS FIRST topic.

Edit: in case you wondered why we're so fanatic about our users not touching WRNLEV or BOMLEV, your fatal error is not caused by the change in atom numbers. CHARMM would likely tell you the real cause of the problem if you wouldn't suppress it by changing WRNLEV .
Posted By: Tarsis Re: Patch for N-sultated Glucosamine - part 2 - 08/21/13 05:57 PM
I'm sorry,

I ran it before with BOMLEV 0 but wanted to test whether it would work with -3.

That's how the script ends with BOMLEV 0

CHARMM> patch amin S 2 setup
ATOM S 2 AGLCNA C AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA O AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA CT AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA HT1 AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA HT2 AND ALL REFERENCES TO IT DELETED.
ATOM S 2 AGLCNA HT3 AND ALL REFERENCES TO IT DELETED.
ATOM S AGLCNA 2 S ADDED.
ATOM S AGLCNA 2 O2 ADDED.
ATOM S AGLCNA 2 O7 ADDED.
ATOM S AGLCNA 2 O8 ADDED.

Message from MAPIC: Atom numbers are changed.
DELTIC: 6 bonds deleted
DELTIC: 11 angles deleted
DELTIC: 13 dihedrals deleted
DELTIC: 2 improper dihedrals deleted
*** LEVEL -3 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.

ABNORMAL TERMINATION
MOST SEVERE WARNING WAS AT LEVEL -3

Attached File
create_disa_nhshb.inp.txt  (780 downloads)
Attached File
nhshb.out.txt  (803 downloads)
Posted By: Kenno Re: Patch for N-sultated Glucosamine - part 2 - 08/21/13 06:02 PM
As mentioned in my last post, you need to remove the WRNLEV command as well. There's still information missing from your output.
Posted By: Tarsis Re: Patch for N-sultated Glucosamine - part 2 - 08/21/13 09:49 PM
Yep, as you said it before, haste makes waste frown

I removed WRNLEV and got what the error was. I will try to fix it by myself and then post the results/questions when they appear.

Thanks again for the patience Kenno.
Posted By: Tarsis Re: Patch for N-sultated Glucosamine - part 2 - 08/22/13 02:36 AM
I think I got it shocked (except by some nasty clashes between the sulfur S1 and O7 and HN nitrogen).

Does anyone know how to fix that?

Thanks all again,

Tarsis

Attached File
patch.tar.gz  (771 downloads)
Attached File
disa.pdb.txt  (848 downloads)
Attached File
nhshb.out.txt  (814 downloads)
Posted By: Kenno Re: Patch for N-sultated Glucosamine - part 2 - 08/22/13 04:01 PM
Now you're talking! The clash can be relieved by editing the values (especially the dihedral) in the IC C1 C2 N HN entry. I speculate it arose after editing IC C1 C2 N S1 without doing the above. To make the hydrogen "follow" automatically when editing the dihedral associated with the heavy atoms, it is recommended to use an improper IC entry, like this:
Code:
IC  C2   S1   *N   HN         0.0000    0.00  120.00    0.00   0.0000
Where the 120 can be changed to -120 depending on the pyramid flip, and the zeroes can be substituted manually with the correct coordinates, or automatically with IC PARAM.

On an unrelated note:
  • You can suppress the charge warning at the beginning of your output by changing the total charge in your topology file like this: PRES AMIN -1.00 .
  • It is good practice to leave the main force field files untouched, and make a private self-contained stream file for any additions.

See the CGenFF files and tutorials for examples illustrating all of the above.
Posted By: Tarsis Re: Patch for N-sultated Glucosamine - part 2 - 08/22/13 05:39 PM
Hi Kenno,

I managed to fix the clash by editing the IC entry as you said, tks by the way for all your help. But now two questions arose.

1) There seems to be a problem with the coordinates for the BGLC atoms (this error does not reflect in anything, just annoys me).

CHARMM> read coor univ unit 1 offset 0
SPATIAL COORDINATES BEING READ FROM UNIT 1
TITLE> NONE
TITLE> *
** WARNING ** NO COORDINATES FOR 1 1 BGLCA C1
** WARNING ** NO COORDINATES FOR 2 1 BGLCA H1
** WARNING ** NO COORDINATES FOR 3 1 BGLCA O1
** WARNING ** NO COORDINATES FOR 4 1 BGLCA HO1
** WARNING ** NO COORDINATES FOR 5 1 BGLCA C5

2) Where can I find impropers that may match those entries?

: No improper parameters for 2 ( SC OC2DP NG2S3 OC2DP )
: No improper parameters for 3 ( NG2S3 SC CC3161 HCP1 )
: No improper parameters for 4 ( SC OC2DP NG2S3 OC2DP )
: A TOTAL OF 3 MISSING PARAMETERS


I will, when done with this parametrization, generate the stream file. Thanks for reminding me that! smile

All the best
Posted By: rmv Re: Patch for N-sultated Glucosamine - part 2 - 08/22/13 06:00 PM
The "NO COORDINATES" error occurs because you may not using READ COOR UNIV correctly, and because the PDB format does not support the 5- and 6-char residue names used by the all36_carb force field.
Posted By: Kenno Re: Patch for N-sultated Glucosamine - part 2 - 08/23/13 02:54 AM
Concerning the impropers, you should never define them on nonplanar/tetrahedral centers (and not even on all planar centers; see this FAQ). So just remove the 3 superfluous IMPR lines from your topology file and you're done (I'm assuming the sulfamate nitrogen is not planar).
Posted By: Tarsis Re: Patch for N-sultated Glucosamine - part 2 - 08/23/13 03:26 PM
Got it, thanks Rick.
Posted By: Tarsis Re: Patch for N-sultated Glucosamine - part 2 - 08/23/13 03:31 PM
Yes, I removed those improper lines but after running a simple minimization and that group clash again. Isn't that cause by the missing impropers?

Attached File
disa-initialmini.crd.txt  (771 downloads)
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disa-initialmini.pdb.txt  (773 downloads)
Attached File
disa-initialmini.psf.txt  (2694 downloads)
Attached File
in_glc.out.txt  (786 downloads)
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Posted By: Kenno Re: Patch for N-sultated Glucosamine - part 2 - 08/23/13 04:42 PM
Nope, it's a (frequently made) mistake in the script that generated the psf file. You need to issue the command "AUTOGENereate ANGLes DIHEdrals" after you're finished patching.
Posted By: Tarsis Re: Patch for N-sultated Glucosamine - part 2 - 08/23/13 06:07 PM
Thanks for the answer and sorry for being such a novice, but now when trying to minimize I get this error:

CHARMM> energy

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec FSWItch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 946 atom pairs and 264 atom exclusions.
There are 0 group pairs and 23 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 1082 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
946 ATOM PAIRS WERE FOUND FOR ATOM LIST
0 GROUP PAIRS REQUIRED ATOM SEARCHES

: No torsion parameters for 72 ( CC3162 CC3161 NG2S3 SC )
: No torsion parameters for 101 ( CC3161 NG2S3 SC OC2DP )
: No torsion parameters for 102 ( CC3161 NG2S3 SC OC2DP )
: No torsion parameters for 103 ( CC3161 NG2S3 SC OC2DP )
: No torsion parameters for 108 ( HCA1 CC3161 NG2S3 SC )
: No torsion parameters for 116 ( HCP1 NG2S3 SC OC2DP )
: No torsion parameters for 117 ( HCP1 NG2S3 SC OC2DP )
: No torsion parameters for 118 ( HCP1 NG2S3 SC OC2DP )
: No torsion parameters for 119 ( SC NG2S3 CC3161 CC3161 )
: A TOTAL OF 9 MISSING PARAMETERS

***** LEVEL -1 WARNING FROM *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

May I add those torsions?


Thanks again

Attached File
in_glc.out.txt  (780 downloads)
Attached File
create_disa_nhshb.inp.txt  (756 downloads)
Attached File
create.out.txt  (919 downloads)
Attached File
Attached File
disa.tar.gz  (728 downloads)
Posted By: Kenno Re: Patch for N-sultated Glucosamine - part 2 - 08/24/13 12:57 AM
I already thought this went a little bit too easy. Yes, all these torsions are required. And validation/optimization would be highly recommended. Especially the C-C-N-S are quite critical.
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