[gmx-users] Problems with pdb2gmx simulating a iron-sulfur cluster
nicolas.martinez at ibs.fr
Mon Apr 23 15:22:37 CEST 2007
Thank you very much Tsjerk. I'm sorry for asking all these questions
but some points are still unclear to me, and I didn't find much
information on the mailing list archives or in the manual that could
Grompp is complaining about the angles because in the .top file there
are no entries for the angle type, because pdb2gmx just creates the
bond, but doesn't specify the type like you told me.
I've edited the ff...bon.itp file as follows but it seems useless.
; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
S S 2 gb_33
NR FE 2 gb_32
; cystine - heme link (is CR1-S, use CH2-S):
S CR1 2 gb_30
; cystine - fs link:
FE S 2 gb_48
[ angletypes ]
CH1 CH2 S 2 ga_15
CH2 S S 2 ga_5
CR1 NR FE 2 ga_33
NR FE NR 2 ga_16
; cystine - heme link (is CH2-S-CR1, use CH2-S-CH2):
CH2 S CR1 2 ga_3
; cystine - heme link (is S-CR1-C/CH2, use CHn-CH2-S):
S CR1 C 2 ga_15
S CR1 CH2 2 ga_15
; cystine - fs link
S FE S 2 ga_47
FE S FE 2 ga_48
where I specified ga_47, ga_48, gb_48...
Is there a way that grompp could take these types or do I have to edit
the topology file manually to specify the type?
It seems strange to me because there are also no entries for the bond
types, and grompp doesn't give me any warnings for that, why?
Thank you again
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