Dear Urszula,
- First, you might be interested by:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
to generate the FF libraries for a (new/modified) dipeptide and its
corresponding central, N-terminal and C-terminal amino acid fragments
by only providing the P2N file of the considered dipeptide.
- then if you provide the right atom names in the P2N file, you do not
need to modify manually the atom names in the mol2 files after
generation.
- for this cycle you could make choices by analogy to other aromatic cycles.
. a CT atom type is for a sp3 carbon -> bad choice for the aromatic cycle
. HC is for an hydrogen which is connected to a sp3 carbon -> bad
choice for the aromatic cycle:
more $AMBERHOME/dat/leap/parm/parm99.dat
CT 12.01 0.878 sp3 aliphatic C
HC 1.008 0.135 H aliph. bond. to C without
electrwd.group
then
NA 14.01 0.530 sp2 N in 5 memb.ring w/H atom (HIS)
NB 14.01 0.530 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
...
CA 12.01 0.360 sp2 C pure aromatic (benzene)
CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring
junction
CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS
CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C
CK 12.01 0.360 sp2 C 5 memb.ring in purines
CM 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6
CN 12.01 0.360 sp2 C aromatic 5&6 memb.ring junct.(TRP)
CQ 12.01 0.360 sp2 C in 5 mem.ring of purines
between 2 N
CR 12.01 0.360 sp2 arom as CQ but in HIS
...
H4 1.008 0.167 H arom. bond. to C with 1 electrwd. group
H5 1.008 0.167 H arom.at C with 2 elctrwd.
gr,+HCOO group
...
S 32.06 2.900 S in disulfide
linkage,pol:JPC,102,2399,98
vdW parameters are identical for all these sp2 carbons
same remark for the different S atom types; even in GAFF I think
CC, NB, CR, H5, CW, H4 and S could be good bets...
regards, Francois
> I have problem with the atom types in my mol2 file,
>
> Could not find angle parameter: HC - CT - S
> Could not find angle parameter: HC - CT - S
> Could not find angle parameter: HC - CT - N
> Could not find angle parameter: S - CT - N
> There are missing parameters.
>
> my mol2 file contains...
>
> 1 CA -0.995684 -0.049134 0.008736 CT 1 TLS
> -0.0334 ****
> 2 HA -0.799138 -0.052416 -1.053068 H1 1 TLS
> 0.0576 ****
> 3 CB -0.099712 -1.111991 0.679776 CT 1 TLS
> -0.1862 ****
> 4 HB2 -0.430116 -2.098640 0.367872 HC 1 TLS
> 0.0919 ****
> 5 HB3 -0.234107 -1.046445 1.752460 HC 1 TLS
> 0.0919 ****
> 6 CG 1.349337 -0.960779 0.324248 CT 1 TLS
> 0.2593 ****
> 7 C -2.453054 -0.425514 0.278900 C 1 TLS
> 0.6347 ****
> 8 O -2.963900 -0.170866 1.336578 O 1 TLS
> -0.5514 ****
> 9 CD 2.346703 -0.594866 1.145530 CT 1 TLS
> -0.2568 ****
> 10 HD2 2.286202 -0.338841 2.182414 HC 1 TLS
> 0.2218 ****
> 11 CE 2.992125 -1.060567 -1.124597 CT 1 TLS
> 0.1351 ****
> 12 HE2 3.502748 -1.213812 -2.055533 HC 1 TLS
> 0.1631 ****
> 13 SD 3.846789 -0.572802 0.290248 S 1 TLS
> -0.0190 ****
> 14 N -0.753783 1.268637 0.538283 N 1 TLS
> -0.4051 ****
> 15 H -1.138646 1.446976 1.442404 H 1 TLS
> 0.2857 ****
> 16 ND1 1.735334 -1.221817 -0.979128 N 1 TLS
> -0.4894 ****
> .<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 7 1
> 4 1 14 1
> 5 3 4 1
> 6 3 5 1
> 7 3 6 1
> 8 6 9 1
> 9 6 16 1
> 10 7 8 1
> 11 9 10 1
> 12 9 13 1
> 13 11 12 1
> 14 11 13 1
> 15 11 16 1
> 16 14 15 1
> .<TRIPOS>SUBSTRUCTURE
> 1 TLS 1 **** 0 **** ****
>
> what is the right atom type for the S and N
>
> best regards
> Urszula
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Received on Tue Nov 29 2011 - 03:00:04 PST
