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parameters for BOC group
#36118 01/02/17 11:02 AM
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Is the parameter for Boc group available.

Re: parameters for BOC group
Hem@1 #36119 01/02/17 05:12 PM
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rmv Online Content
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Yes and no. The atom types and bonded terms are likely available, but there may not be an existing residue topology in the distributed files.

A couple quick searches with grep did not find BOC alone, but there are some complex molecules with the fragment in top_all36_cgenff.rtf which could probably be used as a basis to create a patch (PRES) for replacing an amino group.


Rick Venable
computational chemist

Re: parameters for BOC group
Hem@1 #36120 01/02/17 06:11 PM
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So paramchem.org might work?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: parameters for BOC group
Hem@1 #36121 01/02/17 06:23 PM
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Probably, but I'd use existing fragments from the CGenFF topology file (search for Tert.Butyl) if I needed this for my work. The CGenFF guidelines advise using existing topologies when available, instead of those from cgenff program or its web interface, ParamChem.


Rick Venable
computational chemist

Re: parameters for BOC group
Hem@1 #36151 01/16/17 10:44 PM
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Paramchem would work pretty well with BOC. The penalties should be rather small.


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: parameters for BOC group
Hem@1 #36164 01/19/17 11:57 AM
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Ya,
I have the received the parameter file from CGenFF paramchem in .str format.

the group is defined as "RESI/ scrat". this I have written it as PRES BOC.

(since the atom name C (CG202) should bind with +N of Resi Trp)

in the bond defination i have replaced H02 atom with +N (which earlier binds with C) and following an earlier example i have scripted the setup file as

read sequ card
* peptide seq
*
5
trp thr val ser ala

gener pep setup warn first boc last ct3



the warning in the output as

PARAMETER FILE BEING READ FROM UNIT 99
RDTITL> * PARAMETERS GENERATED BY ANALOGY BY
RDTITL> * CHARMM GENERAL FORCE FIELD (CGENFF) PROGRAM VERSION 1.0.0
RDTITL> *
PARRDR> WARNING: ATOMS IN BOND CG2O OG2D 750.00000 1.22000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG2O OG30 150.00000 1.33400 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG2O N 260.00000 1.30000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG30 CG33 222.50000 1.53800 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG30 OG30 340.00000 1.43000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG33 HGA3 322.00000 1.11100 DONT EXIST
PARRDR> WARNING: ATOMS IN ANGLE OG2D CG2O OG30 90.00000 125.90000 DONT EXIST
**** Warning **** The following extraneous characters
were found while command processing in PARRDR
160.00 2.25760


How should I do the Patch?

Re: parameters for BOC group
Hem@1 #36165 01/19/17 12:02 PM
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Hello,

In the above post I have given various detatils of the input and output (enough to make RMV and lennart red with anger).

my point is how should i patch the BOC group with my the N terminal of the first residue (in my case it is TRP)

Re: parameters for BOC group
Hem@1 #36166 01/19/17 12:04 PM
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* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
* For use with CGenFF version 3.0.1
*

read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*
36 1

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

RESI /scrat 0.000 ! param penalty= 108.000 ; charge penalty= 8.368
GROUP ! CHARGE CH_PENALTY
ATOM C CG2O2 0.557 ! 7.505
ATOM C1 CG331 -0.270 ! 0.622
ATOM O1 OG2D1 -0.456 ! 0.525
ATOM C2 CG331 -0.270 ! 0.622
ATOM O2 OG302 -0.445 ! 8.368
ATOM C3 CG331 -0.270 ! 0.622
ATOM CT CG301 0.232 ! 4.616
ATOM H01 HGA3 0.090 ! 0.025
ATOM H02 HGR52 0.112 ! 2.610
ATOM H03 HGA3 0.090 ! 0.025
ATOM H04 HGA3 0.090 ! 0.025
ATOM H05 HGA3 0.090 ! 0.025
ATOM H06 HGA3 0.090 ! 0.025
ATOM H07 HGA3 0.090 ! 0.025
ATOM H08 HGA3 0.090 ! 0.025
ATOM H09 HGA3 0.090 ! 0.025
ATOM H10 HGA3 0.090 ! 0.025

BOND C O1
BOND C O2
BOND C H02
BOND C1 CT
BOND C1 H03
BOND C1 H06
BOND C1 H09
BOND C2 CT
BOND C2 H04
BOND C2 H07
BOND C2 H10
BOND O2 CT
BOND C3 CT
BOND C3 H01
BOND C3 H05
BOND C3 H08
IMPR C O1 O2 H02

END

read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS
CG2O2 OG2D1 750.00 1.2200 ! PROT adm jr. 5/02/91, acetic acid pure solvent; LIPID methyl acetate
CG2O2 OG302 150.00 1.3340 ! LIPID methyl acetate
CG2O2 HGR52 348.00 1.0960 ! FORH, formic acid, xxwy
CG301 CG331 222.50 1.5380 ! RETINOL TMCH/MECH
CG301 OG302 340.00 1.4300 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide
CG331 HGA3 322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92

ANGLES
OG2D1 CG2O2 OG302 90.00 125.90 160.00 2.25760 ! LIPID acetic acid
OG2D1 CG2O2 HGR52 39.00 119.00 ! FORH, formic acid, xxwy
OG302 CG2O2 HGR52 47.00 105.00 ! /scrat , from OG311 CG2O2 HGR52, PENALTY= 15
CG331 CG301 CG331 58.35 113.50 11.16 2.56100 ! RETINOL TMCH/MECH
CG331 CG301 OG302 75.70 110.10 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha
CG301 CG331 HGA3 33.43 110.10 22.53 2.17900 ! RETINOL TMCH/MECH
HGA3 CG331 HGA3 35.50 108.40 5.40 1.80200 ! PROT alkane update, adm jr., 3/2/92
CG2O2 OG302 CG301 40.00 109.60 30.00 2.26510 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha

DIHEDRALS
OG2D1 CG2O2 OG302 CG301 0.9650 1 180.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide !cacha,corrected kevo, 01/08
OG2D1 CG2O2 OG302 CG301 3.8500 2 180.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide !cacha,corrected kevo, 01/08
HGR52 CG2O2 OG302 CG301 2.0500 2 180.00 ! /scrat , from CG321 CG2O2 OG302 CG301, PENALTY= 108
CG331 CG301 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH
OG302 CG301 CG331 HGA3 0.1600 3 0.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha reset to default by kevo
CG331 CG301 OG302 CG2O2 0.0000 3 0.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha

IMPROPERS
CG2O2 OG2D1 OG302 HGR52 75.0000 0 0.00 ! /scrat , from CG2O2 OG2D1 OG311 HGR52, PENALTY= 1

END
RETURN

Re: parameters for BOC group
Hem@1 #36167 01/19/17 06:10 PM
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Study the existing patch residues, esp. N-terminal patches.

We do appreciate the people who take the time to attach longer listings as .txt files via the Full Reply Screen.



Rick Venable
computational chemist

Re: parameters for BOC group
Hem@1 #36172 01/21/17 07:18 AM
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Hello,

please find the files attached herewith.
file no 2 is named as boc.str
top_all36 and par_all36 are used.

please point me the needful to manage the patch of boc.
the output messages warns me of the missing co-ordinates

Attached Files
boc.txt (3.87 KB, 259 downloads)
boc2.txt (5.26 KB, 278 downloads)
setup.txt (1.45 KB, 305 downloads)
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