Problem with generate output for a covalently bound ligand
Baldeep Khare
I am trying to refine a protein structure with a covalently bound ligand. I am having problem with the generate output. A disulphide bond is formed between the active site Cys and a Sulphur in ligand (named SD for ligand nomenclature). The files that I give in the generate input file are the protein co-ordinate file (with 6 chains A-F, which also has the co-ordinates for the bound ligand, one for each chain), the ligand topology and parameter files among others. I am not sure how to define the disulphide bond but this is what I did:
I modified the protein.top from
PRESidue DISU { disulfide bridge ...CYS CYS...
\DISU/ }
GROUP
MODIfy ATOM 1CB CHARge= 0.19 END
MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END
GROUP
MODIfy ATOM 2CB CHARge= 0.19 END
MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END
ADD BOND 1SG 2SG
ADD ANGLe 1CB 1SG 2SG
ADD ANGLe 1SG 2SG 2CB
ADD DIHEdral 1CA 1CB 1SG 2SG
ADD DIHEdral 1CB 1SG 2SG 2CB
ADD DIHEdral 1SG 2SG 2CB 2CA
END {DISU}
to this....
PRESidue DISU { disulfide bridge ...CYS ETM...
\DISU/ }
GROUP
MODIfy ATOM 1CB CHARge= 0.19 END
MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END
GROUP
MODIfy ATOM 2C1 CHARge= 0.19 END
MODIfy ATOM 2SD TYPE=S CHARge=-0.19 END
ADD BOND 1SG 2SD
ADD ANGLe 1CB 1SG 2SD
ADD ANGLe 1SG 2SD 2C1
END {DISU}
And this is the error I get on running generate input file is as follows:
SCRATC-warning: STORe selections erased.
Status of internal molecular topology database:
-> NATOM= 11606(MAXA= 1000000) NBOND= 11614(MAXB= 1000000)
-> NTHETA= 16479(MAXT= 2000000) NGRP= 1350(MAXGRP= 1000000)
-> NPHI= 6383(MAXP= 2000000) NIMPHI= 5483(MAXIMP= 1000000)
-> NNB= 0(MAXNB= 1000000)
Status of internal molecular topology database:
-> NATOM= 11606(MAXA= 1000000) NBOND= 11613(MAXB= 1000000)
-> NTHETA= 16475(MAXT= 2000000) NGRP= 1350(MAXGRP= 1000000)
-> NPHI= 6380(MAXP= 2000000) NIMPHI= 5481(MAXIMP= 1000000)
-> NNB= 0(MAXNB= 1000000)
Status of internal molecular topology database:
-> NATOM= 11606(MAXA= 1000000) NBOND= 11612(MAXB= 1000000)
-> NTHETA= 16471(MAXT= 2000000) NGRP= 1350(MAXGRP= 1000000)
-> NPHI= 6377(MAXP= 2000000) NIMPHI= 5479(MAXIMP= 1000000)
-> NNB= 0(MAXNB= 1000000)
Status of internal molecular topology database:
-> NATOM= 11606(MAXA= 1000000) NBOND= 11611(MAXB= 1000000)
-> NTHETA= 16467(MAXT= 2000000) NGRP= 1350(MAXGRP= 1000000)
-> NPHI= 6374(MAXP= 2000000) NIMPHI= 5477(MAXIMP= 1000000)
-> NNB= 0(MAXNB= 1000000)
Status of internal molecular topology database:
.
.
.
. ( A CYS 184 SG ) A
( A CYS 184 SG ) 184
( B CYS 184 SG ) B
( B CYS 184 SG ) 184
( C CYS 184 SG ) C
( C CYS 184 SG ) 184
( D CYS 184 SG ) D
( D CYS 184 SG ) 184
( E CYS 184 SG ) E
( E CYS 184 SG ) 184
( F CYS 184 SG ) F
( F CYS 184 SG ) 184
( B CYS 184 SG ) B
( B CYS 184 SG ) 184
( C CYS 184 SG ) C
( C CYS 184 SG ) 184
( D CYS 184 SG ) D
( D CYS 184 SG ) 184
( E CYS 184 SG ) E
( E CYS 184 SG ) 184
( F CYS 184 SG ) F
( F CYS 184 SG ) 184
( C CYS 184 SG ) C
( C CYS 184 SG ) 184
( D CYS 184 SG ) D
( D CYS 184 SG ) 184
( E CYS 184 SG ) E
( E CYS 184 SG ) 184
( F CYS 184 SG ) F
( F CYS 184 SG ) 184
( D CYS 184 SG ) D
( D CYS 184 SG ) 184
( E CYS 184 SG ) E
( E CYS 184 SG ) 184
( F CYS 184 SG ) F
( F CYS 184 SG ) 184
( E CYS 184 SG ) E
( E CYS 184 SG ) 184
( F CYS 184 SG ) F
( F CYS 184 SG ) 184
( F CYS 184 SG ) F
( F CYS 184 SG ) 184
%PATCH-ERR: to be modified atom 2SD not found in molecular structure.
%PATCH-ERR: to be deleted bond 1SG 2SD not found in molecular structure.
%PATCH-ERR: to be deleted angle 1CB 1SG 2SD not found in molecular structure.
%PATCH-ERR: to be deleted angle 1SG 2SD 2C1 not found in molecular structure.
Status of internal molecular topology database:
-> NATOM= 11606(MAXA= 1000000) NBOND= 11604(MAXB= 1000000)
-> NTHETA= 16439(MAXT= 2000000) NGRP= 1352(MAXGRP= 1000000)
-> NPHI= 6353(MAXP= 2000000) NIMPHI= 5463(MAXIMP= 1000000)
-> NNB= 0(MAXNB= 1000000)
%PATCH-ERR: to be modified atom 2SD not found in molecular structure.
%PATCH-ERR: to be deleted bond 1SG 2SD not found in molecular structure.
%PATCH-ERR: to be deleted angle 1CB 1SG 2SD not found in molecular structure.
%PATCH-ERR: to be deleted angle 1SG 2SD 2C1 not found in molecular structure.
Status of internal molecular topology database:
-> NATOM= 11606(MAXA= 1000000) NBOND= 11604(MAXB= 1000000)
-> NTHETA= 16439(MAXT= 2000000) NGRP= 1354(MAXGRP= 1000000)
-> NPHI= 6353(MAXP= 2000000) NIMPHI= 5463(MAXIMP= 1000000)
-> NNB= 0(MAXNB= 1000000)
What am I missing/doing incorrectly? Any suggestions would be much appreciated.
Thank you.
Baldeep.