mohsen ramezanpour wrote:
Dear All
I am using protein-drug binding.
when I am using grompp this error occuring:
Atomtype CR6 not found
and
Atomtype CR5 not found.
by what can I replace these atom types?
Looks like you're mixing and matching force fields. Is your drug topology from
PRODRG? Please heed the caveats here:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
Atom types CR61 and CR51 are from the deprecated ffgmx (don't use it!), while
you're probably trying to combine the output with some form of Gromos96.
Equivalent atom types do exist, but be sure you know what you're doing before
hacking apart a topology.
-Justin
this is my drug.itp file:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CR61 1 LIG C11 1 0.021 13.0190
2 CR61 1 LIG C15 1 0.020 13.0190
3 CB 1 LIG C17 1 0.040 12.0110
4 O 1 LIG F1 1 -0.162 18.9984
5 CR61 1 LIG C16 1 0.021 13.0190
6 CR61 1 LIG C12 1 0.020 13.0190
7 CB 1 LIG C6 1 0.040 12.0110
8 CH1 1 LIG C1 2 0.000 12.0110
9 CH2 1 LIG C2 2 0.000 14.0270
10 CH2 1 LIG C5 3 0.120 14.0270
11 CH2 1 LIG C8 3 0.120 14.0270
12 NL 1 LIG N1 3 0.675 14.0067
13 CH3 1 LIG C18 3 0.085 15.0350
14 CH3 1 LIG C19 4 0.071 15.0350
15 H 1 LIG HAA 4 0.052 1.0080
16 OS 1 LIG O1 4 -0.147 15.9994
17 CR51 1 LIG C7 4 -0.010 13.0190
18 CB 1 LIG C4 4 0.034 12.0110
19 CR61 1 LIG C10 5 0.034 13.0190
20 CB 1 LIG C3 5 0.067 12.0110
21 CR61 1 LIG C9 5 0.034 13.0190
22 CR61 1 LIG C13 5 0.034 13.0190
23 CB 1 LIG C14 5 0.067 12.0110
24 CB 1 LIG C20 5 0.307 12.0110
25 N 1 LIG N2 5 -0.543 14.0067
thanks in advance
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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